Warren sent me the diagnostic logs from his super don hardware. It was running a ROM that I slightly modified to help see what the super don hardware thought it was receiving from the dexter PCB.
After seeks, super don will wait for a status code back from the LD-V1000 that has the high bit set (meaning the value will be >= 128). If the value is not 0xD0 (seek succeeded) it will consider it an error.
Well, the Dexter PCB tries to send back 0xD0 codes, but the super don hardware sees random codes instead, usually 0xF6 but sometimes values like 0xF0, 0xF7, 0xFF, 0xFE. I don't really know what to make of it.