A driver timeout based on leaving the device idle shouldn't be happening. I would have guessed a software problem, but the fact that it also happens with Win98 would seem to indicate otherwise.
Assuming you used the same drive and the same computer under Win98, it appears to be a problem with the drive, or with the computer hardware, or the motherboard BIOS.
The way to find out which would be to try the drive in another computer or try another drive in this computer.
It's amazing how many ways a computer can go wrong. It seems that computers are like snowflakes. No two are alike.