Can you please see if the php.ini file has an error? Issue this command in root SSH:
If there is an error, it will output when you issue that or show nothing. If that happens, then move the existing php.ini file over and recreate it:
Code:
mv /usr/local/lib/php.ini /usr/local/lib/php.ini.bak110613
/scripts/php.ini
At that point, you can do a diff on the files to see what differences they have:
Code:
diff /usr/local/lib/php.ini /usr/local/lib/php.ini.bak110613
Then see if the handler is showing up properly in WHM > Apache Configuration > PHP and SuExec Configuration area to select.