A couple things I'd try, turn off PNP and check the ISA bus speed or clock, it should be 33Mhz. Maybe someone that has a MB based Torq-Cut can chime in on BIOS setting. My TC-3 uses an ISA backplane with an SBC. Normally resetting the BMDC will sort it but I've heard of the mother boards going flakey and causing issues. I'd scrounge up an ISA MB before I replaced the BMDC. I'd also try another PC power supply.
Check this thread:
http://www.cnczone.com/forums/bridge...rd-repair.html