The work around for this is to use your php.in file.. here is an example
running suPHP you can no longer use the .htacess to change any php
All the php_flags in your .htaccess will have to be moved to php.ini, which you will have to create in your public_html directory.
.htaccess » php_flag register_globals off
php.ini » register_globals = Off
The file php.ini will handle all the extra settings you need to set in php.
So, basically you will have to move every command on .htaccess that starts with php_flag.
This is because php is no longer running as an apache module and apache will not handle those directives any longer.
Creating a php.ini file to manipulate the php settings will solve this issue.
You will need to also add this to your .htaccess file to direct it to the php.ini file.