There is a bug in the ini setting handling that surfaces when dynamic extensions are loaded in the system php.ini file.  It can be reproduced with php/apxs and any extension which is built as a shared module.  After the first request handled by a given process, PHP resets all ini values to the compiled-in defaults, and subsequently fails to reload the module-specific ini values from php.ini when further requests arrive.

This bug ONLY affects module-specific ini values configured at the system level, and only when used with extensions that are loaded via php.ini.  It does NOT affect ini settings configured at the per-directory or user level (PHP_INI_PERDIR, PHP_INI_USER), nor does it appear when the extension is built-in or loaded by the user with the dl() function.

Here is a basic PHP configuration that can be used to reproduce the problem.  This is not a real-world example, but it's sufficient for debugging :)

./configure --with-apxs=/usr/sbin/apxs --with-config-file-path=/etc/httpd --enable-session=shared

Install libphp4.so and the session.so module in the appropriate directories, and add these lines to /etc/httpd/php.ini:

extension=session.so
session.save_path = /tmp/blee

Run Apache in single-process mode (httpd -X), and create a php script that calls phpinfo().  The first time phpinfo is loaded, session.save_path will have a local value of /tmp/blee and a master value of /tmp.  After that, it will always show the local and master value as /tmp.