What exactly is it doing? The transformer whistle controller activates the coil on the whistle, and completes the circuit.
With power applied to the whistle, you should be able to move the metal plates below the coil, and the whistle should operate.
If your whistle controller is working properly, a very simple test is that the engine should speed up just a little bit.
Just trying to narrow it down a bit.
Does it do this on straights or just curves. Check out if the tender trucks are somehow shorting.