By manual metering, I mean the following:
When the shutter speed dial is not set to one of the two AE settings, the meter still works. What should happen then is that the meter causes two shutter speed indicators to flash in the viewfinder - one being the recommended shutter speed, with the other being the one that has been manually set. If they are the same, that is what is illuminated and flashing.
If that works, but the AE functions don't, that at least tells you something.
FWIW I've used that prism successfully on both 645 Super bodies and my current 645 Pro body.
The problem may be as simple as a problem with contacts.
Hope you can find a solution.