How does yum need to be configured to work with cPanel ?

cPanel/WHM requires that certain packages be excluded due to the fact that cPanel handles its own installations of services that are separate from what the distros provide. If you have modified the yum.conf, you will want to ensure that the follow excludes do exist:

apache* bind-chroot courier* dovecot* exim* httpd* mod_ssl* mysql* nsd* perl* php* proftpd* pure-ftpd* spamassassin* squirrelmail*

We also strongly recommend using only the vendor-provided distributions, as cPanel is tested only using these packages. 3rd-party repositories such as RPMForge can replace vital parts of the system that cPanel relies on, and cause unexpected results.