cPanel 11.24.4-R32603 - WHM 11.24.2 - X 3.9

Since upgrading to PHP 5.2.8 with Apache 1.3.41 and suPHP enabled, I have noticed custom 'php.ini' files within Document Root no longer work.

Using 'phpinfo.php' to see what is going on, no matter what settings are used there are no changes, compared to Server configuration.

Anyone else noticed this and/or have a resolution?