Hmm... that was a Maxtor harddrive? Right. Something similar happened to me not too long ago. I had this config at the time:
Harddrive 1 - Quantum (2 G
C: win98se
Harddrive 2 - Maxtor DiamondMax Plus D740X (60G
D: w2k
E: w2k server
F: xp pro
G: storage
I started my comp and the maxtor disk was not there. I went into bios and checked it, and it really wasn´t there. Did auto detect. Nothing. Went and got a new battery for the bios even though the mobo was only 2 months old. Did auto detect again. Nothing. Entered the info manually and it found it but on next reboot it was gone again. Then I switched the jumpers on the disks reversing master and slave and on reboot both disks were there. This of course made the system unbootable but when I switched the jumpers back again everything was fine. Never had a problem since then.
I´m thinking maybe this has something to do with Maxtor disks?