The Amiga boots fine with nothing attached, so it can't be the HD (yet).
By "nothing" you mean nothing external, right? The Amiga cannot boot well without the HD attached :-)
There are several SCSI options which can be set in the HD's Rigid Disk Block, like Synchronous, Reselection and so on. Some of them influence the whole SCSI chain. If one of the other drives does not work with one of these options, it might be the reason for the failure.
Where is the Phase5 program you describe? I don't recall seeing it on my HD.
"SCSI Systemdisk" on this page:
http://phase5.a1k.org/invoking the Early Startup screen displays df0:, and the three partitions of a second internal HD, none of which are bootable
Didn't see this before. Is that second internal HD on the P5 SCSI bus, too?
Are you sure that the boot HD has a different SCSI ID than the JAZ drive? Have you checked it?
Are you sure that the internal SCSI config hasn't changed since you used the JAZ drive last time?
IIRC the P5 SCSI kit has the internal devices on one end and the external ones on the other end with the controller in the middle, forming one long SCSI chain. If the termination of the internal devices changed, it might be a reason why adding an external device causes the whole chain to fail.