No, it won't run properly in Win2k (I had a couple of back-and-forth emails with Andy on this; Win2k on my machine as well).
What you can do, though, is plug the gun into an XP pc and run the config utility, do what you need to do on that machine (which IIRC, will probably be reassigning buttons), then move the gun back to the Win2k machine and calibrate it there. That's what I did, and I haven't had any problems, or a need for the config utility, since.