Sorry, had some issues with my new external hard drive (was crashing Explorer) plus one of my buddies came over and we were watching anime.
Anyway, to answer the Quake 3 thing my system had no issues with the sky. Clean install of the game patched to 1.32, running at 1600x1200, 4x AA, 8x AF, no changes to the config file.
Spotch, I would recommend deleting your q3config.cfg file and letting the game rebuild it. That'll reset everything back to default and most likely fix your problem.