Mine is one of the first ACA cards, but it runs almost flawlessly with WHDload, so may be another issue, unless you have a defective card?
I didn't use most of the options other than maprom though. I can check my start up sequence and see if there's an issue.
Is the Indivision a heat concern ? My ACA 030/56 get's heat issues only after a long, warm summer day, so in itself, I doubt it's your accelerator.
Can you check it minus indivision ?