Not sure how the Xorg built-in drivers work as I've always used nvidia but I can give you some suggestions. If you're using fglrx then this advice would probably definitely apply to you.
Installing Mesa alongside another driver that provides it's own libGL can cause issues with Mesa overwriting the libGL symlinks with it's own. Check the output of:
ls -l /usr/lib | grep GL
and see what you've got and where links go.