Most likely this is because you're running 2 different versions of php. If your server CAME with php installed (and http, etc) via rpm, you need to remove those before installing utilities such as cpanel, because CPanel's php and apache binaries are much more reliable and stable, not to mention the fact that cpanel uses their own settings, not those built into rpms.
If you take a look at the phpinfo information, you'll see something like this.
Configuration File (php.ini) Path
Usually, the second version of php is related closely to that path. On newer installs its in /usr/local/lib (or /usr/local/Zend if you're using ZO).
Remove the php and http rpms from your server if you're using them, they're worthless on a cpanel machine.