Becuase they are 6GB drives, I'll venture a guess that they are not too new. That the BIOS recognizes the drives is good. The drives are small enough that there shouldn't be any problems with partition size. If the drives are from different manufacturers, they may have trouble playing nice together, even if all the jumpers are correct.
I have two ideas:
Reset the drives to both be master. Connect the second hard drive to the second IDE channel, temporarily disconnecting the CD-ROM if required. See if windows finds the disk then. You may get away with putting the 2nd drive & the CD-ROM in a master/slave configuration.
You might also try having both drives on the same IDE channel, but set them both to "cable select", rather than master or slave. This works best on newer motherboards, using 80 pin cables.
HTH