I recently had a similar problem. Every time I hit the whistle the train would want to pause briefly. Finally I narrowed it down to the transformer as this did not happen with others or while on another line.
Then I hooked the transformer to another line which has a block signal hooked up directly to the track. This is when I noticed that the lights in it would black out when this happen.
So the end result was that I determined that the transformer brick has some kind of issue. This one was the Z-750. Removed it from service and all is now well.
So I suggest hooking up a bulb to your line and see if you experience the same results.
