aptitude show php-xdebug

I did some more tests this morning and I realized that the problem is not really there, where I've described it.
I've tried the following:
function xdebug($x)
{
if ($x == 1) {
$result = 1;
}
return $result;
}

and realized that the last closing bracket is now marked with -2 (not executable) while it was marked with -1 before. And the conditional's closing bracket isn't there again (which is obviously normal).

So actually not the closing bracket of the condition, but the one of the function is marked falsely as not executed instead of not executable.

This is the correct behaviour. Your original test case does not cover the situation where $x != 1, and hence, the end of the function is never reached. Each function in PHP ends with an implicit "return NULL;":

function name:  xdebug

number of ops:  9

compiled vars:  !0 = $x

line     #* E I O op                           fetch          ext  return  operands

3 0 E > EXT_NOP
1 RECV !0
5 2 EXT_STMT
3 IS_EQUAL 0000002:0000001 !0, 1
4 > JMPZ 0000002:0000001, ->7
6 5 > EXT_STMT
6 > RETURN <true>
8 7 > EXT_STMT
8 > RETURN null

branch: # 0; line: 3- 5; sop: 0; eop: 4; out0: 5; out1: 7
branch: # 5; line: 6- 6; sop: 5; eop: 6; out0: -2
branch: # 7; line: 8- 8; sop: 7; eop: 8; out0: -2
path #1: 0, 5,
path 0000002: 0, 7,
End of function xdebug

From this VLD output, you can see there is a branch instruction on line 4 (the JMPZ), which starts the branches at 5 and 7.
Your tests makes it execute the first branch (with the return true;), but not the second one starting at 7. As your code never touches the implicit "return null;" at the end of the script (op 8), it gets correctly marked as "not executed".