Last time *I* had this problem, the system wasn't detecting ANY drives, and the reason it wasn't detecting them is that the rail putting power to the hard drives had gone tits up and wasn't supplying power fast enough to initialize the drives on boot/reboot.
Replaced the powersupply and everything was hunkydory.
What powersupply do you use, how old is it and what are its numbers?
(amps at 3.3, 5 and 12 volt lines, over all wattage, wattage at each line and combinatoin wattage for 3.3+5 volt lines)
BB