Can you do the following:

1. install valgrind (apt-get install valgrind)
2. on one shell:
   a. export USE_ZEND_ALLOC=1
   b. valgrind /full/path/to/php yourscript.php (script only if necessary)
3. provide the output of valgrind here

if it crashes, do also do this in the same shell:

4. gdb --args /full/path/to/php yourscript.php (script only if necessary)
5. run on the gdb prompt:
   a. run
   b. when it crashes: bt full
6. and provide that output as well.

------- [valgrind output]--------

valgrind /usr/local/bin/php
==20237== Memcheck, a memory error detector.
==20237== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
==20237== Using LibVEX rev 1854, a library for dynamic binary translation.
==20237== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
==20237== Using valgrind-3.3.1-Debian, a dynamic binary instrumentation framework.
==20237== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
==20237== For more details, rerun with: -v
==20237==
==20237== My PID = 20237, parent PID = 2856. Prog and args are:
==20237== /usr/local/bin/php
==20237==
==20237== Invalid free() / delete / delete[]
==20237== at 0x4C2130F: free (vg_replace_malloc.c:323)
==20237== by 0xD96375D: OnUpdateIDEKey (xdebug.c:214)
==20237== by 0x9604A2: zend_alter_ini_entry_ex (zend_ini.c:291)
==20237== by 0x960295: zend_alter_ini_entry (zend_ini.c:249)
==20237== by 0xD963AAC: xdebug_env_key (xdebug.c:353)
==20237== by 0xD963AD1: xdebug_env_config (xdebug.c:366)
==20237== by 0xD96634F: zm_activate_xdebug (xdebug.c:920)
==20237== by 0x94F22C: module_registry_request_startup (zend_API.c:2134)
==20237== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==20237== by 0x944F7F: zend_activate_modules (zend.c:857)
==20237== by 0x8C6AC4: php_request_startup (main.c:1414)
==20237== by 0xA3439B: main (php_cli.c:1088)
==20237== Address 0xe030200 is not stack'd, malloc'd or (recently) free'd
==20237==
==20237== Invalid free() / delete / delete[]
==20237== at 0x4C2130F: free (vg_replace_malloc.c:323)
==20237== by 0xD9664ED: zm_activate_xdebug (xdebug.c:944)
==20237== by 0x94F22C: module_registry_request_startup (zend_API.c:2134)
==20237== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==20237== by 0x944F7F: zend_activate_modules (zend.c:857)
==20237== by 0x8C6AC4: php_request_startup (main.c:1414)
==20237== by 0xA3439B: main (php_cli.c:1088)
==20237== Address 0xe0301f0 is not stack'd, malloc'd or (recently) free'd
==20237==
==20237== Invalid free() / delete / delete[]
==20237== at 0x4C2130F: free (vg_replace_malloc.c:323)
==20237== by 0xD96622F: xdebug_stack_element_dtor (xdebug.c:871)
==20237== by 0xD979978: xdebug_llist_remove (xdebug_llist.c:127)
==20237== by 0xD9690FC: xdebug_execute (xdebug.c:1784)
==20237== by 0x945F91: zend_execute_scripts (zend.c:1194)
==20237== by 0x8C82E2: php_execute_script (main.c:2233)
==20237== by 0xA344E6: main (php_cli.c:1192)
==20237== Address 0xe0301b0 is not stack'd, malloc'd or (recently) free'd
==20237==
==20237== Invalid free() / delete / delete[]
==20237== at 0x4C2130F: free (vg_replace_malloc.c:323)
==20237== by 0xD966261: xdebug_stack_element_dtor (xdebug.c:877)
==20237== by 0xD979978: xdebug_llist_remove (xdebug_llist.c:127)
==20237== by 0xD9690FC: xdebug_execute (xdebug.c:1784)
==20237== by 0x945F91: zend_execute_scripts (zend.c:1194)
==20237== by 0x8C82E2: php_execute_script (main.c:2233)
==20237== by 0xA344E6: main (php_cli.c:1192)
==20237== Address 0xe0301c0 is not stack'd, malloc'd or (recently) free'd
==20237==
==20237== Invalid free() / delete / delete[]
==20237== at 0x4C2130F: free (vg_replace_malloc.c:323)
==20237== by 0xD96375D: OnUpdateIDEKey (xdebug.c:214)
==20237== by 0x95FCEA: zend_restore_ini_entry_cb (zend_ini.c:57)
==20237== by 0x95FE05: zend_restore_ini_entry_wrapper (zend_ini.c:81)
==20237== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==20237== by 0x95FF25: zend_ini_deactivate (zend_ini.c:121)
==20237== by 0x94519E: zend_deactivate (zend.c:919)
==20237== by 0x8C713E: php_request_shutdown (main.c:1606)
==20237== by 0xA34EC8: main (php_cli.c:1373)
==20237== Address 0xe0301e0 is not stack'd, malloc'd or (recently) free'd
==20237==
==20237== Invalid free() / delete / delete[]
==20237== at 0x4C2130F: free (vg_replace_malloc.c:323)
==20237== by 0xD9669CA: zm_post_zend_deactivate_xdebug (xdebug.c:1047)
==20237== by 0x9451DB: exec_done_cb (zend.c:927)
==20237== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==20237== by 0x9451F9: zend_post_deactivate_modules (zend.c:935)
==20237== by 0x8C717A: php_request_shutdown (main.c:1610)
==20237== by 0xA34EC8: main (php_cli.c:1373)
==20237== Address 0xe0301d0 is not stack'd, malloc'd or (recently) free'd
==20237==
==20237== Invalid free() / delete / delete[]
==20237== at 0x4C2130F: free (vg_replace_malloc.c:323)
==20237== by 0xD966A8A: zm_post_zend_deactivate_xdebug (xdebug.c:1066)
==20237== by 0x9451DB: exec_done_cb (zend.c:927)
==20237== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==20237== by 0x9451F9: zend_post_deactivate_modules (zend.c:935)
==20237== by 0x8C717A: php_request_shutdown (main.c:1610)
==20237== by 0xA34EC8: main (php_cli.c:1373)
==20237== Address 0xe0301a0 is not stack'd, malloc'd or (recently) free'd
==20237==
==20237== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 31 from 2)
==20237== malloc/free: in use at exit: 0 bytes in 0 blocks.
==20237== malloc/free: 40 allocs, 47 frees, 1,664 bytes allocated.
==20237== For counts of detected errors, rerun with: -v
==20237== All heap blocks were freed -- no leaks are possible.

------- [gdb run output]--------

gdb --args /usr/local/bin/php
GNU gdb 6.8-debian
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu"...
(gdb) run
Starting program: /usr/local/bin/php
[Thread debugging using libthread_db enabled]
warning: Lowest section in /usr/lib/libicudata.so.38 is .hash at 0000000000000120
[New Thread 0x7f8c3032a710 (LWP 20240)]
glibc detected -: free(): invalid pointer: 0x00007f8c27052200 ***
======= Backtrace: =========
/lib/libc.so.6[0x7f8c297f6928]
/lib/libc.so.6(cfree+0x76)[0x7f8c297f8a36]
/usr/local/lib/php/extensions/debug-non-zts-20090626/xdebug.so[0x7f8c274bf75e]
-(zend_alter_ini_entry_ex+0x20b)[0x9604a3]
-(zend_alter_ini_entry+0x4c)[0x960296]
/usr/local/lib/php/extensions/debug-non-zts-20090626/xdebug.so(xdebug_env_key+0x9a)[0x7f8c274bfaad]
/usr/local/lib/php/extensions/debug-non-zts-20090626/xdebug.so(xdebug_env_config+0x23)[0x7f8c274bfad2]
/usr/local/lib/php/extensions/debug-non-zts-20090626/xdebug.so(zm_activate_xdebug+0x18)[0x7f8c274c2350]
-[0x94f22d]
-(zend_hash_apply+0x7e)[0x956c5b]
-[0x944f80]
-(php_request_startup+0x218)[0x8c6ac5]
-[0xa3439c]
/lib/libc.so.6(__libc_start_main+0xe6)[0x7f8c297a11a6]
-[0x439b69]
======= Memory map: ========
00400000-00efd000 r-xp 00000000 03:01 402948 /usr/local/bin/php
010fc000-011a6000 rw-p 00afc000 03:01 402948 /usr/local/bin/php
011a6000-011c6000 rw-p 011a6000 00:00 0
7f8c26f57000-7f8c271a3000 rwxp 7f8c26f57000 00:00 0
7f8c271a3000-7f8c271ad000 r-xp 00000000 03:01 635564 /lib/libnss_files-2.7.so
7f8c271ad000-7f8c273ad000 ---p 0000a000 03:01 635564 /lib/libnss_files-2.7.so
7f8c273ad000-7f8c273af000 rw-p 0000a000 03:01 635564 /lib/libnss_files-2.7.so
7f8c273af000-7f8c273b1000 rwxp 7f8c273af000 00:00 0
7f8c273b1000-7f8c274b5000 rwxp 7f8c273b1000 00:00 0
7f8c274b5000-7f8c274e8000 r-xp 00000000 03:01 489068 /usr/local/lib/php/extensions/debug-non-zts-20090626/xdebug.so
7f8c274e8000-7f8c276e7000 ---p 00033000 03:01 489068 /usr/local/lib/php/extensions/debug-non-zts-20090626/xdebug.so
7f8c276e7000-7f8c276eb000 rw-p 00032000 03:01 489068 /usr/local/lib/php/extensions/debug-non-zts-20090626/xdebug.so
7f8c276eb000-7f8c27818000 rwxp 7f8c276eb000 00:00 0
7f8c27818000-7f8c27b61000 r--p 00000000 03:01 407957 /usr/lib/locale/locale-archive
7f8c27b61000-7f8c27b70000 r-xp 00000000 03:01 394232 /usr/lib/libtasn1.so.3.0.15
7f8c27b70000-7f8c27d70000 ---p 0000f000 03:01 394232 /usr/lib/libtasn1.so.3.0.15
7f8c27d70000-7f8c27d71000 rw-p 0000f000 03:01 394232 /usr/lib/libtasn1.so.3.0.15
7f8c27d71000-7f8c27d8a000 r-xp 00000000 03:01 394330 /usr/lib/libsasl2.so.2.0.22
7f8c27d8a000-7f8c27f8a000 ---p 00019000 03:01 394330 /usr/lib/libsasl2.so.2.0.22
7f8c27f8a000-7f8c27f8b000 rw-p 00019000 03:01 394330 /usr/lib/libsasl2.so.2.0.22
7f8c27f8b000-7f8c27f8e000 r-xp 00000000 03:01 394219 /usr/lib/libgpg-error.so.0.3.0
7f8c27f8e000-7f8c2808d000 ---p 00003000 03:01 394219 /usr/lib/libgpg-error.so.0.3.0
7f8c2808d000-7f8c2808e000 rw-p 00002000 03:01 394219 /usr/lib/libgpg-error.so.0.3.0
7f8c2808e000-7f8c28135000 r-xp 00000000 03:01 392150 /usr/lib/libgnutls.so.26.4.6
7f8c28135000-7f8c28335000 ---p 000a7000 03:01 392150 /usr/lib/libgnutls.so.26.4.6
7f8c28335000-7f8c28340000 rw-p 000a7000 03:01 392150 /usr/lib/libgnutls.so.26.4.6
7f8c28340000-7f8c28385000 r-xp 00000000 03:01 395593 /usr/lib/libldap_r-2.4.so.2.1.0
7f8c28385000-7f8c28584000 ---p 00045000 03:01 395593 /usr/lib/libldap_r-2.4.so.2.1.0
7f8c28584000-7f8c28587000 rw-p 00044000 03:01 395593 /usr/lib/libldap_r-2.4.so.2.1.0
7f8c28587000-7f8c28589000 rw-p 7f8c28587000 00:00 0
7f8c28589000-7f8c28597000 r-xp 00000000 03:01 395592 /usr/lib/liblber-2.4.so.2.1.0
7f8c28597000-7f8c28797000 ---p 0000e000 03:01 395592 /usr/lib/liblber-2.4.so.2.1.0
7f8c28797000-7f8c28798000 rw-p 0000e000 03:01 395592 /usr/lib/liblber-2.4.so.2.1.0
7f8c28798000-7f8c287c9000 r-xp 00000000 03:01 395589 /usr/lib/libidn.so.11.5.37
7f8c287c9000-7f8c289c9000 ---p 00031000 03:01 395589 /usr/lib/libidn.so.11.5.37
7f8c289c9000-7f8c289ca000 rw-p 00031000 03:01 395589 /usr/lib/libidn.so.11.5.37
7f8c289ca000-7f8c289cc000 r-xp 00000000 03:01 635241 /lib/libkeyutils-1.2.so
7f8c289cc000-7f8c28bcb000 ---p 00002000 03:01 635241 /lib/libkeyutils-1.2.so
7f8c28bcb000-7f8c28bcc000 rw-p 00001000 03:01 635241 /lib/libkeyutils-1.2.so
7f8c28bcc000-7f8c28bd3000 r-xp 00000000 03:01 394817 /usr/lib/libkrb5support.so.0.1
7f8c28bd3000-7f8c28dd3000 ---p 00007000 03:01 394817 /usr/lib/libkrb5support.so.0.1
7f8c28dd3000-7f8c28dd4000 rw-p 00007000 03:01 394817 /usr/lib/libkrb5support.so.0.1
7f8c28dd4000-7f8c28dfc000 r-xp 00000000 03:01 394272 /usr/lib/libpcre.so.3.12.1
7f8c28dfc000-7f8c28ffb000 ---p 00028000 03:01 394272 /usr/lib/libpcre.so.3.12.1
7f8c28ffb000-7f8c28ffc000 rw-p 00027000 03:01 394272 /usr/lib/libpcre.so.3.12.1
7f8c28ffc000-7f8c29061000 r-xp 00000000 03:01 394226 /usr/lib/libgcrypt.so.11.4.4
7f8c29061000-7f8c29260000 ---p 00065000 03:01 394226 /usr/lib/libgcrypt.so.11.4.4
7f8c29260000-7f8c29263000 rw-p 00064000 03:01 394226 /usr/lib/libgcrypt.so.11.4.4
7f8c29263000-7f8c29354000 r-xp 00000000 03:01 391423 /usr/lib/libstdc++.so.6.0.10
7f8c29354000-7f8c29553000 ---p 000f1000 03:01 391423 /usr/lib/libstdc++.so.6.0.10
7f8c29553000-7f8c29559000 r--p 000f0000 03:01 391423 /usr/lib/libstdc++.so.6.0.10
7f8c29559000-7f8c2955c000 rw-p 000f6000 03:01 391423 /usr/lib/libstdc++.so.6.0.10
7f8c2955c000-7f8c2956f000 rw-p 7f8c2955c000 00:00 0
7f8c2956f000-7f8c2957f000 r-xp 00000000 03:01 635582 /lib/libresolv-2.7.so
7f8c2957f000-7f8c2977f000 ---p 00010000 03:01 635582 /lib/libresolv-2.7.so
7f8c2977f000-7f8c29781000 rw-p 00010000 03:01 635582 /lib/libresolv-2.7.so
7f8c29781000-7f8c29783000 rw-p 7f8c29781000 00:00 0
7f8c29783000-7f8c298cd000 r-xp 00000000 03:01 635581 /lib/libc-2.7.so
7f8c298cd000-7f8c29acc000 ---p 0014a000 03:01 635581 /lib/libc-2.7.so
7f8c29acc000-7f8c29acf000 r--p 00149000 03:01 635581 /lib/libc-2.7.so
7f8c29acf000-7f8c29ad1000 rw-p 0014c000 03:01 635581 /lib/libc-2.7.so
7f8c29ad1000-7f8c29ad6000 rw-p 7f8c29ad1000 00:00 0
7f8c29ad6000-7f8c29aec000 r-xp 00000000 03:01 635235 /lib/libgcc_s.so.1
7f8c29aec000-7f8c29cec000 ---p 00016000 03:01 635235 /lib/libgcc_s.so.1
7f8c29cec000-7f8c29ced000 rw-p 00016000 03:01 635235 /lib/libgcc_s.so.1
7f8c29ced000-7f8c29e3f000 r-xp 00000000 03:01 394808 /usr/lib/libxml2.so.2.6.32
7f8c29e3f000-7f8c2a03e000 ---p 00152000 03:01 394808 /usr/lib/libxml2.so.2.6.32
7f8c2a03e000-7f8c2a048000 rw-p 00151000 03:01 394808 /usr/lib/libxml2.so.2.6.32
7f8c2a048000-7f8c2a049000 rw-p 7f8c2a048000 00:00 0
7f8c2a049000-7f8c2a082000 r-xp 00000000 03:01 24702 /usr/lib/libxslt.so.1.1.24
7f8c2a082000-7f8c2a281000 ---p 00039000 03:01 24702 /usr/lib/libxslt.so.1.1.24
7f8c2a281000-7f8c2a283000 rw-p 00038000 03:01 24702 /usr/lib/libxslt.so.1.1.24
7f8c2a283000-7f8c2a298000 r-xp 00000000 03:01 635579 /lib/libnsl-2.7.so
7f8c2a298000-7f8c2a497000 ---p 00015000 03:01 635579 /lib/libnsl-2.7.so
7f8c2a497000-7f8c2a499000 rw-p 00014000 03:01 635579 /lib/libnsl-2.7.so
7f8c2a499000-7f8c2a49b000 rw-p 7f8c2a499000 00:00 0
7f8c2a49b000-7f8c2a65a000 r-xp 00000000 03:01 397004 /usr/lib/libmysqlclient.so.15.0.0
7f8c2a65a000-7f8c2a85a000 ---p 001bf000 03:01 397004 /usr/lib/libmysqlclient.so.15.0.0
7f8c2a85a000-7f8c2a8a5000 rw-p 001bf000 03:01 397004 /usr/lib/libmysqlclient.so.15.0.0
7f8c2a8a5000-7f8c2a8a6000 rw-p 7f8c2a8a5000 00:00 0
7f8c2a8a6000-7f8c2a8b0000 r-xp 00000000 03:01 24660 /usr/lib/libicuio.so.38.1
7f8c2a8b0000-7f8c2aab0000 ---p 0000a000 03:01 24660 /usr/lib/libicuio.s
Program received signal SIGABRT, Aborted.
[Switching to Thread 0x7f8c3032a710 (LWP 20240)]
0x00007f8c297b4ed5 in raise () from /lib/libc.so.6

------- [gdb bt full output]--------

(gdb) bt full
#0 0x00007f8c297b4ed5 in raise () from /lib/libc.so.6
No symbol table info available.
#1 0x00007f8c297b63f3 in abort () from /lib/libc.so.6
No symbol table info available.
0000002 0x00007f8c297f1388 in ?? () from /lib/libc.so.6
No symbol table info available.
0000003 0x00007f8c297f6928 in ?? () from /lib/libc.so.6
No symbol table info available.
0000004 0x00007f8c297f8a36 in free () from /lib/libc.so.6
No symbol table info available.
0000005 0x00007f8c274bf75e in OnUpdateIDEKey (entry=0x7f8c27018e80, new_value=0x7f8c26fec720 "root", new_value_length=4, mh_arg1=0x0, mh_arg2=0x0, mh_arg3=0x0, stage=4)
at /opt/XDEBUG_2_1_0beta1/xdebug.c:214
No locals.
0000006 0x00000000009604a3 in zend_alter_ini_entry_ex (name=0x7f8c274deec5 "xdebug.idekey", name_length=14, new_value=0x7fff6a80cec8 "root", new_value_length=4, modify_type=4, stage=4, force_change=0)
at /opt/php-5.3.2RC1/Zend/zend_ini.c:291
ini_entry = (zend_ini_entry ) 0x7f8c27018e80
duplicate = 0x7f8c26fec720 "root"
modifiable = 7 '\a'
modified = 0 '\0'
0000007 0x0000000000960296 in zend_alter_ini_entry (name=0x7f8c274deec5 "xdebug.idekey", name_length=14, new_value=0x7fff6a80cec8 "root", new_value_length=4, modify_type=4, stage=4)
at /opt/php-5.3.2RC1/Zend/zend_ini.c:249
No locals.
0000008 0x00007f8c274bfaad in xdebug_env_key () at /opt/XDEBUG_2_1_0beta1/xdebug.c:353
ide_key = 0x7fff6a80cec8 "root"
0000009 0x00007f8c274bfad2 in xdebug_env_config () at /opt/XDEBUG_2_1_0beta1/xdebug.c:366
config = 0x0
parts = (xdebug_arg ) 0x0
i = 32652
0000010 0x00007f8c274c2350 in zm_activate_xdebug (type=1, module_number=52) at /opt/XDEBUG_2_1_0beta1/xdebug.c:920
orig = (zend_function *) 0xe6982d
idekey = 0x100000031 <Address 0x100000031 out of bounds>
dummy = (zval *) 0x8aef36
0000011 0x000000000094f22d in module_registry_request_startup (module=0x7f8c27024e00) at /opt/php-5.3.2RC1/Zend/zend_API.c:2134
No locals.
0000012 0x0000000000956c5b in zend_hash_apply (ht=0x11c5640, apply_func=0x94f1f2 <module_registry_request_startup>) at /opt/php-5.3.2RC1/Zend/zend_hash.c:673
result = 0
p = (Bucket ) 0x7f8c2701fc80
0000013 0x0000000000944f80 in zend_activate_modules () at /opt/php-5.3.2RC1/Zend/zend.c:857
No locals.
0000014 0x00000000008c6ac5 in php_request_startup () at /opt/php-5.3.2RC1/main/main.c:1414
orig_bailout = (jmp_buf *) 0x7fff6a80c410
bailout = {{jmpbuf = {10702864, -5510940994126348779, 4430656, 140734980212736, 0, 0, -5510940994164097515, 5511245153361329685}, mask_was_saved = 0, saved_mask = {__val = {0, 0,
140240079995354, 1, 0, 9291095, 9201475, 140239967928896, 10702864, 4294967295, 18503168, 18611616, 18191360, 140734980212744, 4313575380, 140734980211728}}}}
retval = 0
0000015 0x0000000000a3439c in main (argc=1, argv=0x7fff6a80c808) at /opt/php-5.3.2RC1/sapi/cli/php_cli.c:1088
orig_bailout = (jmp_buf *) 0x0
bailout = {{jmpbuf = {10702864, -5510940993979548139, 4430656, 140734980212736, 0, 0, -5510940994132640235, 5511244974534295061}, mask_was_saved = 0, saved_mask = {__val = {
140240001543651, 140239967956952, 140240079978156, 4294967296, 140240079978156, 40, 140240080792952, 29, 55, 2269477195, 140240079979364, 140240010794840, 140239272149003, 35460581,
140734980211936, 140734980212328}}}}
exit_status = 0
c = -1
file_handle = {type = ZEND_HANDLE_FP, filename = 0xe82605 "-", opened_path = 0x0, handle = {fd = 699205280, fp = 0x7f8c29ad06a0, stream = {handle = 0x7f8c29ad06a0, isatty = 1786824528, mmap = {
len = 140734980212504, pos = 4131212846, map = 0x7fff6a80c700, buf = 0x0, old_handle = 0x7f8c302685ae, old_closer = 0}, reader = 0x7f8c3032eec0, fsizer = 0x7fff00000001, closer = 0}},
free_filename = 0 '\0'}
behavior = 1
reflection_what = 0x0
orig_optind = 1
orig_optarg = 0x0
arg_free = 0x7fff6a80ce4d "/usr/local/bin/php"
arg_excp = (char **) 0x7fff6a80c808
script_file = 0x0
interactive = 0
module_started = 1
request_started = 0
lineno = 0
exec_direct = 0x0
exec_run = 0x0
exec_begin = 0x0
exec_end = 0x0
param_error = 0x0
hide_argv = 0
ini_entries_len = 110

I have just made a guess at fixing it, as I can't actually reproduce this. Can you try the latest SVN version please to see if it's fixed?

I'm still having the same problem...

Bleh, made a little mistake in my instructions, can you please try the following:

1. on one shell:
   a. export USE_ZEND_ALLOC=0 (I had put "1" here before)
   b. valgrind /full/path/to/php yourscript.php (script only if necessary)
2. provide the output of valgrind

I've checked out and compiled it again, and suprise : it seems to give less errors, though it still does not work :/

---------------[valgrind output]----------------------

valgrind /usr/local/bin/php empty.php
==3047== Memcheck, a memory error detector.
==3047== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
==3047== Using LibVEX rev 1854, a library for dynamic binary translation.
==3047== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
==3047== Using valgrind-3.3.1-Debian, a dynamic binary instrumentation framework.
==3047== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
==3047== For more details, rerun with: -v
==3047==
==3047== Invalid free() / delete / delete[]
==3047== at 0x4C2130F: free (vg_replace_malloc.c:323)
==3047== by 0xD96F6BD: zm_activate_xdebug (xdebug.c:713)
==3047== by 0x94F22C: module_registry_request_startup (zend_API.c:2134)
==3047== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==3047== by 0x944F7F: zend_activate_modules (zend.c:857)
==3047== by 0x8C6AC4: php_request_startup (main.c:1414)
==3047== by 0xA3439B: main (php_cli.c:1088)
==3047== Address 0xe036190 is not stack'd, malloc'd or (recently) free'd
==3047==
==3047== Invalid free() / delete / delete[]
==3047== at 0x4C2130F: free (vg_replace_malloc.c:323)
==3047== by 0xD96F3D2: xdebug_stack_element_dtor (xdebug.c:637)
==3047== by 0xD97EF00: xdebug_llist_remove (xdebug_llist.c:127)
==3047== by 0xD971743: xdebug_execute (xdebug.c:1287)
==3047== by 0x945F91: zend_execute_scripts (zend.c:1194)
==3047== by 0x8C82E2: php_execute_script (main.c:2233)
==3047== by 0xA344E6: main (php_cli.c:1192)
==3047== Address 0xe548f90 is not stack'd, malloc'd or (recently) free'd
==3047==
==3047== Invalid free() / delete / delete[]
==3047== at 0x4C2130F: free (vg_replace_malloc.c:323)
==3047== by 0xD96F404: xdebug_stack_element_dtor (xdebug.c:643)
==3047== by 0xD97EF00: xdebug_llist_remove (xdebug_llist.c:127)
==3047== by 0xD971743: xdebug_execute (xdebug.c:1287)
==3047== by 0x945F91: zend_execute_scripts (zend.c:1194)
==3047== by 0x8C82E2: php_execute_script (main.c:2233)
==3047== by 0xA344E6: main (php_cli.c:1192)
==3047== Address 0xe0654c0 is not stack'd, malloc'd or (recently) free'd
==3047==
==3047== Invalid free() / delete / delete[]
==3047== at 0x4C2130F: free (vg_replace_malloc.c:323)
==3047== by 0xD96E33D: OnUpdateIDEKey (xdebug.c:201)
==3047== by 0x95FCEA: zend_restore_ini_entry_cb (zend_ini.c:57)
==3047== by 0x95FE05: zend_restore_ini_entry_wrapper (zend_ini.c:81)
==3047== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==3047== by 0x95FF25: zend_ini_deactivate (zend_ini.c:121)
==3047== by 0x94519E: zend_deactivate (zend.c:919)
==3047== by 0x8C713E: php_request_shutdown (main.c:1606)
==3047== by 0xA34EC8: main (php_cli.c:1373)
==3047== Address 0xe036170 is not stack'd, malloc'd or (recently) free'd
==3047==
==3047== Invalid free() / delete / delete[]
==3047== at 0x4C2130F: free (vg_replace_malloc.c:323)
==3047== by 0xD96FB9A: zm_post_zend_deactivate_xdebug (xdebug.c:816)
==3047== by 0x9451DB: exec_done_cb (zend.c:927)
==3047== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==3047== by 0x9451F9: zend_post_deactivate_modules (zend.c:935)
==3047== by 0x8C717A: php_request_shutdown (main.c:1610)
==3047== by 0xA34EC8: main (php_cli.c:1373)
==3047== Address 0xe0654a0 is not stack'd, malloc'd or (recently) free'd
==3047==
==3047== Invalid free() / delete / delete[]
==3047== at 0x4C2130F: free (vg_replace_malloc.c:323)
==3047== by 0xD96FC5A: zm_post_zend_deactivate_xdebug (xdebug.c:835)
==3047== by 0x9451DB: exec_done_cb (zend.c:927)
==3047== by 0x956C5A: zend_hash_apply (zend_hash.c:673)
==3047== by 0x9451F9: zend_post_deactivate_modules (zend.c:935)
==3047== by 0x8C717A: php_request_shutdown (main.c:1610)
==3047== by 0xA34EC8: main (php_cli.c:1373)
==3047== Address 0xe548fc0 is not stack'd, malloc'd or (recently) free'd
==3047==
==3047== ERROR SUMMARY: 6 errors from 6 contexts (suppressed: 31 from 2)
==3047== malloc/free: in use at exit: 0 bytes in 0 blocks.
==3047== malloc/free: 40 allocs, 46 frees, 1,664 bytes allocated.
==3047== For counts of detected errors, rerun with: -v
==3047== All heap blocks were freed -- no leaks are possible.

This bug still doesn't make sense. To me it looks like a compiler optimized out some code. I don't know which one you have but you might want to upgrade it. If that doesn't help, I am afraid I'll have to ask for access to the machine to debug it.

I'm compiling on a local virtual machine, I can open an access for you if you need it.

I would appreciated that; please mail access details directly to derick@xdebug.org .

I've sent you the access details in a mail with "Access for bug 0000526" as subject.

I had a quick look today on your VM, but still no luck. I don't understand why I can't get the same behaviour locally either. I'll try more later.

Closing this one as "not a bug", because you wrote:

The "bad guy" was dmalloc.
When I compiled without using --enable-dmalloc option, everything went OK.

Dmalloc is another memory allocation checker, which will most likely conflict with both the Zend memory manager and glibc anyway. We'll simply not support it instead.