Swap out the 80 wire IDE (I hope you are using an 80 wire IDE cable!!). sound to me like the IDE cable is fobarred. Does the bios find both the drives everytime? Try booting into the bios at POST and see if the two IDE hd's are always recognized. The cable swap first, Bios reset will be next (pulling out the Cmos battery) and then, possibly a bios flash.
Noli Nothis Permittere Te Terere!!
EVGA 680i, Dual EVGA 8800GT'S (650/950), 4 gigs OCZ DDR2 1066, Intel Q9450 at 3.8 Ghz, Koolance Water Cooled, Dual Plextor16x DL DVD+/-RW. Dual WD 250gb 16mb Cache Sata 3.0. 3DMark06 score = 19,168.