It sounds like you forgot to set the jumpers on the drives correctly. The cd or dvd drive connected to the end of the ide cable is always set as master with the center drive set at the slave postition. If you have never set a jumper you simply look at the rear of the drive casing for a small rectangular opening near where the ide cable plugs in.
You will see a small plastic cap covering two pins on two rows of small metal pins there. A small pair of tweezers or very small pliers are used to lightly grab the small cap and pull it out easy and far enough to move it over to the pair with MA or master seen marked in the drive casing. That would be for the drive plugged in at the end of the cable.
For the drive connected with the middle connector you would move the "jumper" over to the SL or slave position to assign that correctly. Often drives come in with the jumper set to the "cable select" position if not set to the master.
Glad to see it wasn't a hardware problem. 