Hi Thomas,
Just to make it clear, are you saying that the Quantum hard drive does show up when the CD Rom drive is not connected? Is the CD Rom drive terminated? Although with some devices, things may work fine when you don't have a SCSI terminator at one end of the chain, other devices will have problems with no terminator. The E-mu samplers have a built-in terminator but you also need one for the end of the chain.
HTH,
Fernando