Intel USB drivers are built into win2k. It sounds like something is sharing the usb resources, which is confusing win2k, making it not able to see the usb properly.
With an intel bios, it doesn't display the resource list in the second post screen, like other motherboard makers, so it is harder to discern what is going on. You might try checking in the bios to see if you can tell the usb to use a specific interupt. You might also remove all the cards except video, and disable any onboard devices, and then try booting into windows and doing a add new hardware search.