But where were you hooking the battery to? Directly into the trailer plug, using a female trailer plug for the connection? Otherwise you are leaving the most failure prone part of the setup out of the equation (trailer plug and socket on truck). Anywhere between the magnets and the truck wiring could be the problem. FWIW, when my trailer brakes were acting up it was the same symptoms on my F250 with integrated controller and behind my IH 4700 or LT9000 with Tekonsha Prodigy brake controllers.