it works with neither the a3640 nor with a known working Cyberstorm MkIII
Couple more possiblities....
I'm assuming your Agnus is socketed, try removing and resetting that if you havn't already. A shorted CIA chip will cause the same failure but since those are soldered to the mother board it makes them harder to test or replace. (Not to mention it's become harder to find a replacement chip.) I know you said they didn't seem hot, but that doesn't always tell the whole story. I've replaced dozens over the years repairing 500/2000's and a few 1200/4000's. I don't think I ever saw one go bad in a 3000, but I was probably just lucky. A couple were suspiciously hot, most were not. If you don't hang extra hardware off your serial/parallel ports and don't normally dis/re-connect drives with power on then the CIA's are probably ok, but they still have my attention. Unfortunatly you've done much testing already and are running out of easy fixes. Have you removed the motherboard from the case and checked for any thing suspicious on the bottom of the motherboard?
Plaz