I have installed freepbx on top of a cPanel server. The problem I am running into is kind of wierd. The main index page loads up, but when clicking on any of the links I get errors (Internal Server Error). I have looked in the log files and didn’t really see anything that would help. I have googled till I was blue in the face 
lol… Please help.
internal server erros mean a couple things: process limit has been exceeded and the .htaccess file has bad coding.
What os are you using?
centOS 5.5 I can’t image the process limit has exceeded (there isn’t really anything running on this machine, no websites or anything). I will try and take a look at the .htaccess and see if i notice anything.