Are these Drives IDE or SATA? you mention IDE so i'm curious if this is the case, do you have the jumpers on "Cable Select" or might you have them both set to master or slave because if this is the situation, it would explain why you could only see one at a time.
And your sure the BIOS is only detecting one or the other?
If your drives are SATA, then which SATA ports are plugged in? for instance, SATA 5 and SATA 6 have DVD's on them but only SATA5 will display in the BIOS. If you switch the DVD's around, the other DVD works on SATA 5 and again nothing on SATA 6. If this is the situation, Try only one Drive plugged into each of these ports at a time and try another SATA cable to rule that out with 100% certainty.