Okay, It might be that the system drive is slower then the jaz. Is the jaz drive set up as a bootable disk? Does the ext box have a termination block on the outside?
It might be double termed now?
But the conflict is with the system drive being read first.
Try removing the cartridge, then first power up the ext box, power up the amiga, after it's booted, insert the cartridge, let it spin up and...hopefully be accessible...