Yes, the way you initially swapped them would be the same effect as if you swapped the wires from the transformer at either the base of the accessory or the transformer end, so it won't help here.
On the similar 6-24153 model I just looked at, the diode is under shrink tubing on the red wire before it leads into the black housing of the gearbox, Just like Lionel Parts said. (I was probably thinking of another accessory when I suggested the diode was inside the case itself. Unless that small difference could have happened when they made the 32988)
Good luck. It sounds a lot like it simply was manufactured wrong, with the wire including the diode on the wrong terminal of the motor.
-Dave
