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I have a 05 PSD and when i hook up a trailer to the 7 round connector i get only running lights. No brake lights or turn signals. I tried one trailer that had brakes and they worked just not lights. There others were small trailers that i use the 4 flat to 7 round adapter. I havent tried the four flat on the truck. I tried my brothers super duty with the same adapter and his worked everything. I have aftermarket brake controler but figured they should work with out this installed. Plus it is a plug and play system. Just trying to get ideas where I should start looking.
Have you checked the fuses? There are seperate fuses for the trailer lights and the truck lights. The other thing I would check is the wiring harness itself. I had this same problem, sort of, when I first got my truck. They installed the wrong harness from the factory. The harness that was on there wa for the pre-99 HD trucks. The connector plugged in, but the wiring was incorrect. New harness, no problem.
Other than that, check where the harness is plugged in under the truck, right near the spare tire and make sure it's tight and clean.