maybe you should try running Q3 in win98. i had many problems with UT running in win2k (VERY slow framerates with gts2, 500+ping, couldn't connect to servers, general protection faults), but my friend didn't. we have almost the same setup, but his ran flawlessly. however, when i switched back down to win98, all the problems disappeared and i ran 60+fps framerates with all the servers working. i dunno, just must be bad luck or something, but try dualbooting 98se and if the problems still isn't fixed, then screw 98se and i have no idea.
PIII 450, 128 RAM, i740 (the i740 was last year's best midrange 2d card, so ha!) voodoo2 sli, 4.8X toshiba DVD, 4x4x20 cd-rw