You have good testing methodology. Not everyone does so it's usually worth suggesting if it has not already been specified.
I suspect that the PDS terminator requirement could vary from machine to machine, even within the exact same model. Apple's specifications say that something must be there to terminate the bus. In reality, the lack of a card may not cause enough ringing on the bus to cause a problem, in some cases. But in other cases it probably does, because if it did not, it seems unlikely that Apple would have gone to the trouble to fabricate and include PDS terminator cards. Power Computing included the terminators with their 8100 clones as well.
So, yes, I'd try terminating the PDS slot with some kind of compatible card and see if that makes a difference. It that doesn't work, then check the CPU for cracks and try replacing the heat sink grease if the CPU isn't cracked.
I suspect that the PDS terminator requirement could vary from machine to machine, even within the exact same model. Apple's specifications say that something must be there to terminate the bus. In reality, the lack of a card may not cause enough ringing on the bus to cause a problem, in some cases. But in other cases it probably does, because if it did not, it seems unlikely that Apple would have gone to the trouble to fabricate and include PDS terminator cards. Power Computing included the terminators with their 8100 clones as well.
So, yes, I'd try terminating the PDS slot with some kind of compatible card and see if that makes a difference. It that doesn't work, then check the CPU for cracks and try replacing the heat sink grease if the CPU isn't cracked.