Check your jumper configuration on your drives. Also make sure everything is seated firmly. In my experience it usually has to do with jumpers, the bios can sometimes struggle past incorrectly jumpered drives, but perfomance can take a real beating.
Rereading that again, you also may have a low battery on your mainboard.
I had this problem with one of my newer drives....it has some sort of delay in spin down and spin up..when the computer restarted you could hear the drive spin down and not back up...no idea how to fix it though since it was my secondary drive....
odd thing was a few mins later it would spin up...and be visible in windows which surprised the hell out of me