Well, you can always try Reformatting it with the built in Operating System Format.. Since I have no 2000 boxes around anymore, I cannot tell you for sure that it will work with the older OS, but I have had to reformat my old MP3 Flash Stick Player before, and it worked... (Now I use a Zune, so if I loose it, I will have to try something more extreme, like updating the firmware..)
Now, all that being said, I also have a vast array of memory sticks that are quite dead, and formatting them does me no good at all...
Also, it could even be the USB ports themselves that are causing your issues.. one quick fix might be to update the drivers, or just uninstall the USB devices (Device Manager) and then reinstall them, just by rebooting your PC.
I have a great link for solving USB problems, since my website is down for repairs.. read through this for some help with USB:
For XP: http://www.usbman.com/WinME%20USB%20Guide.htm
For 2000: http://www.usbman.com/Win2000.htm