PHP Extensions loading but not working correctly.

Hello

We are running CloudLinux with CPanel, We have a website that is complaining that it can not find class "PDO" or the loader "IonCube" after extensive testing we can see both are installed and working, HOWEVER they only work if the php.ini is manually created with the extensions specified inside of them in the users directory for example:

Code:

zend_extension="/usr/local/IonCube/ioncube_loader_lin_5.6.so"
extension=pdo.so
extension=pdo_sqlite.so
extension=pdo_mysql.so

Notes:
Tweak Settings -> PHP -> Ioncube is Enabled
We have removed reinstalled Ioncube, Rebuilt Apache Numerious times.
There are no errors in the apache logs file either and not logs or messages when apache is restarted.

Any ideas? Thanks in advance.