So it seems you were correct Bruce.
I turned the ProtoSound volume to zero and then removed the body of the tender. Listening closely to the clicks while changing directions I've noticed that there are a pair of clocks for each direction change (one when power is interrupted and one when it is brought up again). However, when the engine goes into reverse there is a 3rd click of a slightly different tone immediately following the 2nd click. On attpting to move forwards ,this 3rd click does not occur.
I assume this is the relay/transistor that is being referred to. Unfortunately, I have no idea how to replace the part or even identify which component of the board is the one responsible. My two local train stores both tell me I would have to send the engine off to MTH to get it serviced, which (since I live in Canada) is most likely going to be an expensive fix.
At this point, is it worth it to simply upgrade the engine to Proto Sound 3 with one of the upgrade kits I've seen online before?