php.ini memory issue server wide & ignoring all settings

Hello,

I may be able to save some posts by first saying that I have gone as far as recompiling PHP to with alter_ini turned off in the PHP build so the php.ini is system wide and not affected by directory level ini directives. No .htaccess or directory level php.ini will fix it.

The wp_config, php.ini and httpd.cnf all have values in excess of 64 M and yet WP is stuck on file size exceeds the value set in the php.ini. php.info shows that the ini loading is usr/local/lib/php.ini and shows the correct values with no other ini loading. I have ran php.info in the root and admin across 8 domains, 6 of which have uploaded thousands of files in excess of this limit.

However, mycloud, opencart and an array of custom coded scripts have no such issues at all. What could be happening that affects only WP, install independant and server wide? I am on a CentOS LAMP stack with latest WHM Stable and PHP 5.3. Sites smbsms.com, bisouwedding.com (new), no-trespassing.org etc.

I have been tracking this down and trying to figure it out for 2 days now. I am at a total loss.