Jeff, I agree that the input transformer seems like a very unlikely culprit, I'm just sort of at my wits end here!
The polarity switch does act peculiar. I wrote about this on the very thread if you scroll up. Engaging the polarity switch on the bad unit drops the signal to basically zero.
I've checked the DC resistant between red and orange pads with the transformers completely taken out of the circuit and there is certainly a difference. The good module shows 20k Ohm between those pads, the bad one shows OL (overload), basically an open circuit or at least up into the tens of mega ohm region.