^+1, Good thinking there pastit, that never even crossed my mind.
@op - If the drive's have the large ribbin, usally grey, sytle connection to the motherboard, they are IDE drives and there is a jumper on the back of each of them to set one to master and the other to a slave drive, most drives have them clearly labeled, if not look up the drive model number on google for instuctions.
Here is a pic of the jumpers:
Keep in mind this may not be the solution to your problem, but it is a VERY GOOD place to start. Again nice work pastit.