I would look at your jumper settings on the back of each drive. You need to configure the drives so that one is a master/primary drive connected to the end of the IDE/ribbon cable and the other is a slave/secondary drive connected to the plug in the middle of the ribbon cable. Usually the hard drive will have a small diagram on where to place the jumper to set it as a master(MS) or a slave(SL) or cables select(CS).
See this article for more info:
http://www.pchell.com/hardware/masterslaveorcableselect.shtml