I had an island error on my GI a few years ago. It turned out to be a loose connection between a wire and an IDC connector (I think mine was on a motor controller board under the playfield). It would come and go as I did diagnostics and poked around in the machine, presumably from me moving the wiring harness around. Your problem might be something similar, where it has come and gone as you changed MPU boards due to jiggling around the connectors and the wiring harness. It might be worth a look at all the connectors, and even the solder joints on the corresponding pins on the boards, to see if something might be loose.