Can you try debugging with a small script? And provide the full xdebug remote log file? (Feel free to remove it first, to remove the stuff that's already in there)

I created an empty project, only contain a single index.php which does the following (also shown in screenshoot):
<?php

$a = 1;
$b = 2;
$c = $a + $b;

echo 'Result: ' + $c;

xdebug_break();

?>
Its only break on the line 9, which is xdebug_break(), but not on the line 5 and 7....

Just in case, my php.ini extension are follows, which I hadn't changed since the day it was working:

zend_extension=/usr/lib64/php/modules/xdebug.so
;extension=xdebug.so
xdebug.remote_log="/tmp/xdebug.log"
xdebug.profiler_enable = 1
xdebug.remote_enable=on
;xdebug.remote_host=10.197.15.61
;xdebug.remote_host=10.197.9.59
xdebug.remote_port=9000
xdebug.remote_autostart=1
xdebug.idekey=php-vs
xdebug.remote_handler=dbgp
xdebug.remote_mode=req
xdebug.remote_connect_back=On

Also phpInfo()

xdebug

xdebug support enabled
Version 2.3.2
IDE Key 97C383C0

Supported protocols Revision
DBGp - Common DeBuGger Protocol $Revision: 1.145 $

Directive Local Value Master Value
xdebug.auto_trace Off Off
xdebug.cli_color 0 0
xdebug.collect_assignments Off Off
xdebug.collect_includes On On
xdebug.collect_params 0 0
xdebug.collect_return Off Off
xdebug.collect_vars Off Off
xdebug.coverage_enable On On
xdebug.default_enable On On
xdebug.dump.COOKIE no value no value
xdebug.dump.ENV no value no value
xdebug.dump.FILES no value no value
xdebug.dump.GET no value no value
xdebug.dump.POST no value no value
xdebug.dump.REQUEST no value no value
xdebug.dump.SERVER no value no value
xdebug.dump.SESSION no value no value
xdebug.dump_globals On On
xdebug.dump_once On On
xdebug.dump_undefined Off Off
xdebug.extended_info On On
xdebug.file_link_format no value no value
xdebug.force_display_errors Off Off
xdebug.force_error_reporting 0 0
xdebug.halt_level 0 0
xdebug.idekey php-vs php-vs
xdebug.max_nesting_level 256 256
xdebug.max_stack_frames -1 -1
xdebug.overload_var_dump On On
xdebug.profiler_aggregate Off Off
xdebug.profiler_append Off Off
xdebug.profiler_enable On On
xdebug.profiler_enable_trigger Off Off
xdebug.profiler_enable_trigger_value no value no value
xdebug.profiler_output_dir /tmp /tmp
xdebug.profiler_output_name cachegrind.out.%p cachegrind.out.%p
xdebug.remote_autostart On On
xdebug.remote_connect_back On On
xdebug.remote_cookie_expire_time 3600 3600
xdebug.remote_enable On On
xdebug.remote_handler dbgp dbgp
xdebug.remote_host localhost localhost
xdebug.remote_log /tmp/xdebug.log /tmp/xdebug.log
xdebug.remote_mode req req
xdebug.remote_port 9000 9000
xdebug.scream Off Off
xdebug.show_exception_trace Off Off
xdebug.show_local_vars Off Off
xdebug.show_mem_delta Off Off
xdebug.trace_enable_trigger Off Off
xdebug.trace_enable_trigger_value no value no value
xdebug.trace_format 0 0
xdebug.trace_options 0 0
xdebug.trace_output_dir /tmp /tmp
xdebug.trace_output_name trace.%c trace.%c
xdebug.var_display_max_children 128 128
xdebug.var_display_max_data 512 512
xdebug.var_display_max_depth 3 3

I got it working by uninstall PHP Version 5.4.41 from my Centos machine and reinstall PHP 5.5.27 (php55u).

I am not sure, but probably is because how xDebug works. Its first interpret in Centos's PHP 5.4.41 and send debug information to my local windows machine which runs PHP 5.6.8 and interpret the debug information with my source code.

Maybe that's why it won't stop at breakpoint I provided in IDE?

I think it could have to do with file name cases on the file system. I've improved this in later Xdebug versions so perhaps that's what it is. I am closing this one out, as it seems you've resolved it for your use case.