Possibly a cable? Ill have the same problems on one of my CD drives, and then eventually the whole thing disappears along with a Win2K message yelling at me for unplugging stuff.
It's a rare thing so I don't care much, but my guessis I either have a bad cable, or a bad spot on the motherboard. The hard drive (seldom used) connected to that same cable goes as well at the same time.
I'd swap cables on it for a while and see if that changes anything. At least you can knock one piece out of the chain.