php.ini not updating properly

Installed PHP-FPM via easy apache under PHP Extensions. Then used convert in PHP manager. All worked great. The only issue we seem to have is if we now forexample change any php.ini files using PHP editor. For eg. We needed to remove a functions like eval() under disable_functions in the php.ini for all sites on the server and did it using Multi PHP Editor and it updates on the global php.ini file but when checking phpinfo or testing on any website it does not update? I then checked the PHP conf files of each site and it does not update those files? If we edit the files manually and make the changes it reverts later back. What are we doing wrong?