If you have phpsuexec enabled, make sure you also set the relevant configuration in a local php.ini file.
Otherwise this sounds like a PHP issue, in which case all the documentation can be found at
www.php.net.
Specifically take a look at
http://pl.php.net/features.file-upload, use the information available to you to determine the cause of the problem.
If you still believe it to be a Cpanel issue, post back with details such as the symptoms that lead you to believe it is a Cpanel issue so that others have something to work with to help you.
