So if you run just the one Hard Drive, the CD works? Yes? I would start by switching the IDE cable and see what happens. Might be as simple as a bad cable! Otherwise, you might have to go nuclear and back up your critical data and reformat and do a fresh install of your OS.
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.