It would be helpful to know what you have done to diagnose the problem with your controller and transformer set-up; such as checking for loose wiring connections, shorts to ground, maybe swapping connections between controller and transformer, and/or checking AC voltages at different points in the electrical path from the controller thru the transformer to the track starting at the source.
After checking for loose connections at the power source and for electrical shorts between power and common with a multi-meter, I suggest checking AC voltages at different points- with track wiring connected and then disconnected.
