Well, usually win2k game performance is just a little bit behind win9x performance.. A few fps usually. I read an anandtech article recently where they compared nvidias driver performance in win2k and win9x. In just about every test the win2k installation came within a handful of FPS to the win9x one.. so i don't expect the half performance thing is in the least bit normal..
try re-installing the drivers.. directx etc. make sure you have the agp drivers for your mobo installed
I don't know why homeworld and cataclysm can't use opengl in win2k. They could in NT4.. i shall have to research this.