I've noticed a few people have had a problem with the Joystick disappearing under Windows 2000.
The symptoms typically are that the joystick doesn't work in any games. If you go into control panel->game controllers, the joystick shows up as "unknown" for about 2 seconds, and then shows "OK". This repeats itself everytime you bring up the game controllers option in control panel.
This problem only started for me after I flashed my BIOS. This also caused all my PNP devices to have their resources re-allocated. One thing I noticed was that the IRQ on my SB16 had changed from IRQ 5 to IRQ 7. Changing this back to 5 restored the proper operation of my joytick.
Yay!