While you're at it, you might want to whack your card into AGP mode, PCI mode severly limits the speed of your card. Not sure how much that would show with XSI, but it would certainly show a noticable different in any game or benchmark.
I doubt that has anything to do with the problem, but it's something worth sorting out 
XSi 2.01 has known issues with the OpenGL 1.1 drivers on win2k, I believe, get hold of the XSI update, or upgrade your openGL drivers to 1.3, again, I'm not sure if that's the issue, it's hard to tell as it's really quite a strange problem. Almost sounds like a memory leak of some kind.
Is your system well ventilated? With your setup, you'll need to keep it nice and cool, or it will start freezing/shutting down when it overheats.