Thanks for the posting. Does this only apply to the /etc/php.ini? What about if you copy the /etc/php.ini file locally and edit it, like users do on web hosting services where they aren't root so they can't restart Apache?
If users on shared hosting services have access to some type of personal php.ini, then php isn't being loaded into apache as a module but is instead being run as a cgi via suPHP or something similar.
I see in your original post:
PHP 4.3.9 (cgi)
Do you have more info on how apache is serving php pages? Maybe search your httpd.conf file (and any included files) for php...
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