I run FS One on Win 2000 Pro. I never had a complication with the USB interface.
Just put on my trouble shooter cap as I read your message and I'll let you know if I think of something.
The easiest but also hardest solution is to simply reinstall the OS... I'm guessing some other software installation at some point has foobered something with the USB. It happens... for example I tried a new firewall a while back then after was impossible to reinstall my old firewall. It can be good to have a registry fixer like TuneUp Utilities to avoid these things, but might be too late for that to help.
Again I'll try and think of something.
Hopefully I or someone else comes up with something so you don't need to reinstall windows (which for sure
should fix it (and reset whatever's been foobered) as I know the USB interface works in Win2000).
Hang in there, I hope you're flying soon
edit: how new is your system btw?
Possible that it could be a little too new for Win2000, but I'm assuming you bought it with Win2K on it.