SCSI is often a bugger to get working on some systems. I used to spend ages configuring SCSI based workstations under NT4 and it was often a nightmare to get it all working correctly.

As for the A3000, I've not sure what the issue could be. What version of Kickstart does your A3000 have? WHat kickstart screen appears when you boot it without an HD present? The only thing I can think is that the earlier kickstart versions in the A3000 used a bootstrap loader which needs to load the kickstart rom from the HD rather than from a rom chip and you would need to set this up on the new HD. But that is just a wild guess.

How have you tried to setup the SCSI HD? As you have a PC SCSI card you have the option to set the HD up using WinUAE and then move the drive back to the A3000 once it is done.