I'm not an expert in old Mac startup sequences, but I do know that normally, when you start up, the system polls all of the ports to see what's connected and such. From what you say, it would seem that your Quantum will not respond to the system on that level again, once it's been initialized. So it has to power-off and back on to "reset"… Yes, that's vague, but like I said, what the hell do I know?
All we do know is that it's the HDD and NOT the computer, since it behaves the same in different systems.
Does it work properly if you power off and immediately power on again? That would seem to confirm something is resetting in the HDD. BUT, when you say "Makes no difference if you boot off this drive or another", do you mean the computer still hangs just because the Quantum is connected? Is that with another drive before or after the Quantum in the SCSI chain?
This sounds like a job for SuperMacTron…