I am not sure if you have two ide cables or one, If you are using a different ide cable for IDE 1 and 2, The one that can't be seen by the system, could be a cable select ide cable.
Examine the cable, there will be a rectangular hole punched in the flat cabling that completely cuts one strand of wire in the ide cable. If thats the case, the unit plugged into it has to be set to cable select in order to be reconized. The middle IDE connector sets for the c drive and the end connector would be the d drive. This is backwards if you have a
real cable select ide cable, which has a crossover wire on it.
Sound confusing?? It can be a real riot when ghosting an old drive to a new drive, you could end up with two blank drives

and it gets worse from there.
So if you have one of those, I suggest you get rid of it.