SCSI and IDE(ATA) are 2 seperate busses. SCSI doesn't use the master/slave system. It uses ID 7 as the bus controller and then the drives are assigned IDs by jumper 0 through 6 and optionally, depending on the SCSI type, 8-15. IDE/ATA on the other hand use master/slave so if it's the only drive on the chain it doesn't matter how you have it jumpered. It sounds like the IDE busses are disabled in the BIOS. BE WARNED! Some systems such as older IBMs that come with a SCSI boot drive do NOT like having an ATA drive attached when booting off SCSI.
Hope this helps.