Just to cover the basics when you say that each variable channel powers one-half of the layout.
Is each half electrically separated from the other ? If you shut down one channel, have you checked the other half of the track with a meter to see if voltage is somehow still passing through ?
Have you tried swapping variable channels to each half and see if the issue still persists ?
Have you tried using fixed outputs to each half and lowering the voltage using the transformer handles and see if the issue resolves itself ?
