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I have a 2005 F250 Diesel with a factory trailer brake controler and tow package. I also had a Fifth wheel installed, along with a second 7 pin plug in the bed(i Assume its piggy backed). the other day while trying to bring my horse home, i lost brake connection to the trailer everything else worked, but the controller didn't see the trailer. i wasn't going far, so i took it easy and durring the 12 mile trip, the controller saw the trailer sometimes and other times the brakes locked up. the trailer is a 2005 2 horse sundowner.
i checked the fuses for the conrtoller and they were all good any thoughts would be great
Check and see if you have any brake or tail lights. if not, it is probably a bad ground connection where the trailer plugs into the truck. try cleaning the contacts on both sides with a wire brush or sandpaper.
I'd be inclined to start out by checking the resistance on that ground. That's where most electric brake problems are, and that switching from full-on locked to totally dead is classic for varying resistance on your ground because it's going through your hitch rather than the wire. You shouldn't have more than a few ohms resistance between the truck and the trailer, or it's not working right. If you don't want to go through taking meter readings and finding a good, clean, exposed part on both your truck and trailer, then just hook up your trailer plug without hitching up and see if all your lights and brake controller are functioning properly. That will also get you the ability to try out the factory plug rather than the one you had put in the bed, too. This whole thing could just be a sloppy ground on that new plug or a cold joint somewhere.
If you have the correct voltage at the plug I would take the wheels off and check the magnets on the brakes, if it wore down and fell off or wore down it can cause the control to lose connection and get it back until it loses connection for good. We had this problem on my hot shot trailer, the dealer installed a dexter 10k magnet hanger on one wheel when we have dexter 12k axles we lost 2 magnets before I pulled off all four brakes to see where the problem was and ended up being that. But it would do the same thing yours is doing.
if you lose ground truck-trailer, then what happens is if the controller dumps the output, to ground using pullup resistors on the output, the lights will backfeed thru the brake magnets and then to ground in the controller.
This prevents the controller from seeing the leak current it sends thru the magnets as 'connected' and it keeps the brakes on at all times. eventually something brakes.
I found this on voyager controllers while drawtite seems to be immune (ne'er took em apart to see how they individually ticked)
I have found the electrical plug sometimes doesn't make a good connection between vehicle and pigtail. i use an electrical contact cleaner on both the connector on vehicle and cable connector. This gets the dirt and crud off the connecton and it works.