zend_alter_ini_entry_ex has several failure paths. It would be helpful to know which one is being triggered. Can you investigate this? You can try first by starting apache under gdb with the -X option.

It will take some time for me to debug into php code, even because the problem 
happen only on the ~5% of requests, my users notice the problem only with my 
server are under load.

For now, I can add this: we have this problem since migrated from 5.2.6 to 5.3.10.

It breaks always at zend_ini.c:300

The data i pass is always correct, but sometimes i get a FAILURE.

Breakpoint 3, zend_alter_ini_entry_ex (name=0x7f2de6128199 "open_basedir", 
name_length=13,
    new_value=0x7f2debd02e48 "/tmp/:/usr/share/php/:.:/home/www-
data/musitalia.com/html/", new_value_length=58, modify_type=4, 
stage=16, 
force_change=0)
    at /root/php-5.3.10/Zend/zend_ini.c:300
300                     return FAILURE;
(gdb) bt full
#0  zend_alter_ini_entry_ex (name=0x7f2de6128199 "open_basedir", name_length=13,
    new_value=0x7f2debd02e48 "/tmp/:/usr/share/php/:.:/home/www-
data/musitalia.com/html/", new_value_length=58, modify_type=4, 
stage=16, 
force_change=0)
    at /root/php-5.3.10/Zend/zend_ini.c:300
        ini_entry = 0x7f2debb35d30
        duplicate = 0x7f2debaf3140 'Z' <repeats 59 times>, "N\230D\300ZQ\twe-
\177"
        modifiable = 7 '\a'
        modified = 1 '\001'
#1  0x00007f2de77f00d0 in zend_alter_ini_entry (name=0x7f2de6128199 
"open_basedir", name_length=13,
    new_value=0x7f2debd02e48 "/tmp/:/usr/share/php/:.:/home/www-
data/musitalia.com/html/", new_value_length=58, modify_type=4, 
stage=16)
    at /root/php-5.3.10/Zend/zend_ini.c:249
No locals.
#2  0x00007f2de6126c1d in mod_vhost_ldap_translate_name (r=0x7f2debd01570) at 
mod_vhost_ldap_ng.c:862
        reqc = 0x7f2deb4b0510
        conf = 0x7f2deba31038
        core = 0x7f2deb9695e8
        ld = 0x0
        realfile = 0x0
        alias = 0x0
        i = 0
        ret = 0
        str = {0x0, 0x0, 0x0}
        ldapmsg = 0x0
        vhostentry = 0x0
        openbasedir = 0x7f2debd02e48 "/tmp/:/usr/share/php/:.:/home/www-
data/musitalia.com/html/"
        include = 0x7f2debd02e08 "/tmp/:/usr/share/php/:.:/home/www-
data/musitalia.com/html/"

I assume you're using the prefork SAPI, as the stack trace shows you're not using ZTS. In that case, I find strange your claim this is a concurrency issue. More likely, the problem would be in your module and I don't know anything about Apache modules lifecycle to even guess where the problem could be.

You could try passing another value for stage as the ini update handler for open_basedir can never fail for stages PHP_INI_STAGE_STARTUP, PHP_INI_STAGE_SHUTDOWN, PHP_INI_STAGE_ACTIVATE,PHP_INI_STAGE_DEACTIVATE, but this would most likely just mask the underlying problem. You can also try running Apache under valgrind with --trace-children and see if you get something.

I don't think it's a my  module problem because with 5.2 i dont have this problem 
(i did the sames tests for 5.3, same apache, same config), i moved to 5.3 from less 
than one month. I don't think it's a concurrency related issue too, the failure are 
too much rare i think.

I did a diff between 5.2 and 5.3 and saw there are major changes to 
fopen_wrapper.c, and i have this problem only for open_basedir, that's why i opened 
the bug.

I'll try with other stages in the hope this can help.

The fact it worked in 5.2 doesn't imply your code had no bug. It may mean that a bug has always existed, but by luck it wasn't triggered by 5.2. Of course, if you could identify the specific commit that triggers the problem, it could shed light on this problem. If you can automate the tests, you can easily run something a bisection procedure to find such commit.

I really would like debug php and find what's wrong.

For now i moved from PHP_INI_STAGE_RUNTIME to PHP_INI_STAGE_ACTIVATE and the 
problem disappeared.

But now i get this in logs when apache stops:
[]/Zend/zend_ini.c(278) :  Freeing 0x7F63E5BB4908 (72 bytes), script=/home/www-
data/mesogeamag.it/html/index.php
[]/Zend/zend_ini.c(279) :  Freeing 0x7F63E5BB49A8 (64 bytes), script=/home/www-
data/mesogeamag.it/html/index.php
[]/Zend/zend_alloc.c(2454) : Actual location (location was relayed)
[]/Zend/zend_hash.c(250) :  Freeing 0x7F63E5BB4A40 (84 bytes), script=/home/www-
data/mesogeamag.it/html/index.php
[]/Zend/zend_ini.c(289) :  Freeing 0x7F63E5BB4AE8 (64 bytes), script=/home/www-
data/mesogeamag.it/html/index.php


Thank you for help