Oh Jeebus it's been too long. I used to know this stuff inside out. I can't even recall where the priority setting is.
What SCSI card are you using? I assume the 3000 and Jaz worked fine together before the move?
Sometimes active termination on one end doesn't play well with passive termination on the other end (your HD most likely). I can't grok why, but it's been known to happen. Also are there any resistor packs for termination on the card itself? Does it have any active termination capability?
o What happens if you leave the Jaz connected (but off) then power up the computer? Try one of those SCSI-bus rescanning utils. HDtoolbox might have one IIRC.
o Alternately, with the cpu off, turn on the Jaz unit and insert a cart(ridge). Give it time to fully spin up. Then turn on the cpu. Does it all behave differently from above? What if you never insert a cart-- any difference?