I just realized, as soon as you upgrade to PHP 5.1.x this is not working aymore. It looks like the php.ini file is completely ignored. How can I then turn on or off register_globals for single domains? I'm also running phpsuexec.
I do remember reading a post on the cpanel forums, and I don't know who it was that said it, but apparently the cpanel developers disabled this customized php.ini setting in their PHP 5 phpsuexec release. Apparently it was a feature that was never meant to be used, but users found out about it anyway.
As far as a solution, I have none. Switch to suPHP is my only suggestion, I find it to be a better solution anyway.