Not at all sure I understand what the A500 case has to do with this ... Is anything left of the A500. Being very careful you can actually run the A1200 motherboard from the bench with no case. I have one running in a cardboard box. The diagnostic would be to strip everything away until you just had the motherboard and then work up. I say this because I had an issue like this once and it turned out to be a pin shorting out on the case as I closed the case. Open the case it worked, close the case it didn't.
Sorry if I missed something....
Here are some images of the cardboard Amiga and an A1200 in a 2000 case.
http://www.commodore-amiga-retro.com/amiga/amiga_scuzz185.htmhttp://www.commodore-amiga-retro.com/amiga/amiga_scuzz222.htm
