Try Re-seating the card that connects the ISA slot from the computer mother board to the I/O Dpram card. It may be worth checking the ISA card for bad solder joints. The computer mother board could be going bad. Check for vented electrolytic caps. Hopefully it is not a mother board issue. They are hard to find these days.
Sounds like you have tried everything I can think of as far as hardware is concerned. One thing that sounds suspicious to me if the error "Failed to create empty document". I have only seen that error when my MMI software got corrupted in the process of testing spare motherboards. Have you tried setting the control board type to "None" in the INI Editor just to see if the software runs clean without the VME rack involved? Annother thing I noticed when testing spare mother boards is you have to make sure the bios is set to have the hardware handle plug and play or it will never comunicate with the VME rack. I realize that the failure started with your original motherboard but this would be something to check on your spare. Could you let me know what the cause of this problem was when you get it figured out? Feel free to email me if you have any quetsions Good Luck!