I have two comments on that odd Bachmann circuit design.
First, I'd ask you to double check that PCB to see if there is anything connected BETWEEN the two thermal fuses. There appears to be a trace on the board going under one of them in the middle (on the left side of the board) and then snaking off and around down to R2, among other places. There could be a reason for having two. I seriously doubt they just put two breakers in series.
Second, as to the design of having two power transistors, one for each polarity, have to you tried flipping the direction switch
while the throttle is up to see how the circuit reacts? It's hard to tell just from looking at the schematic, but maybe using the two
transistors creates a circuit that will gradually ramp down and back up in the opposite direction without jarring the train.