Hi Steve,
If you are systematically swapping components from one tram to the other, you should eventually find the faulty component that transfers the fault to the good tram.
If you were using a spare controller (instead of swapping from one tram to the other) were the controller parameters set exactly the same as the good tram?
It might be worth checking the +5V supply and the throttle signal output voltages on both trams to see if they are both the same.
Also check the Phase wire/Hall Sensor wire configurations to see if there is any difference there.
Could the brakes be binding (or tight wheel bearings etc.) on the problem tram?
I'm not sure what else to suggest, as you seem to have already covered most of the likely causes.
Alan