Everything works when headlights are not on, but when I turn headlights on and hit the brakes the trailer lights turn off? when headlights are on the flashers and lights work but when I hit the brake turns off trailer lights? It has the harness plugged into the factory hook up. Any help would be much appreciated!

 

Verify that the vehicle harness is putting out the correct signals to all the pins, use this as a guide to what you should be seeing on each pin...
http://www.etrailer.com/faq-wiring.aspx

 

kinda sounds like a bad ground. you will have to test truck and trailer grounds, that is where I would start. or you can just run new grounds.