It sounds to me like your brake controller may need to be replaced or that you have a damaged wire or pin in the wiring harness. I recommend checking the pins and wire to ensure no damage or lose connections and using some Dielectric Grease for Electrical Connectors, 2 oz. Item # 11755 on the pins.
If checking all the wiring and pins doesn't fix your issue then I recommend replacing the brake controller with the Tekonsha Voyager Trailer Brake Controller - 1 to 4 Axles - Proportional #... view full answer...