I have a really similar problem. When I first installed 2000, q3 worked fine, and faster than ever, even though only 1 processor was being used. Now it wont even start right. The game will begin but as soon as it gets to the menu it lags so bad i can barely get out of the game, and if I dont get out fast itll lock up my machine tight. Nor can i play movies succesfully, or run anything that seems to ahve anything to do with directx, including the directx diagnostic tests.
I am running a duel 466 with BP6, sblive, leadtek winfast geforce 256 and 128 megs. No change in drivers work, and neither does reinstalling 2000, it does this with both liveware installed and without it. It has confused the hell out of me, and I hate having to reboot into 98 just to play q3.