Each time you reinstall the driver (fglrx) for some reason, be sure you do "eselect opengl set ati" again, even if the ebuild says it's doing it for you. I've been hit by that dozens of times. Can't be sure if it's your problem but it might worth a try.
Besides that, if you have both installed, make sure (using lsmod) that only fglrx OR radeon+drm is loaded, and that it matches the one in your xorg.conf. Otherwise funny things will happen. -- Jesús Guerrero
