I could be wrong here and the Net-nanny software we run on the proxy here prevents me from looking at game sites but I think 1.33b is the latest patch for Quake3. If I'm wrong it's just punkbuster you're having trouble with you could try upgrading it by itself. I know that if you're trying to play RTCW online you're going to have to do that.
As for Quake2, what are you using for an installer? I highly recommend the icculus.org installer since it's far and away the best looking version of Quake2 I think you'll find. I've been using RH8 & 9 with an NVidia card with no issues whatsoever.
What distro are you using?