Light on auto trailer lights don't work. Turn to on and all OK

It is reasonable to believe that the stock truck wires are likely not at issue, and the added on trailer wires are causing some kind of feedback to the lighting control that is sharing that a concern is present and needs troubleshooting. Check for any blown fuses, and any open circuits -- you mentioned you checked for shorts, but what about lack of continuity? You'll need an DVOM (digital voltmeter ohmmeter) to check the circuit, as well as a wiring diagram. No easy answers, other than checking fuses, to be found.