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It was nice today, and I couldn't resist anymore, so I hooked the '05 F250 V-10 I purchased in November to my camper to see how it towed. Even better than the '99 I crashed!!! Didn't even know the trailer was there, the factory trailer brake controller worked flawlessly. The only thing is I have no brake lights, turn signals, or hazard flashers. Everything else seems to be fine. I climbed under the truck just to have a look, and there is black tape in a few places where it probably shouldn't be, there are some open ended wires, and it appears the looms have shaken loose from their attached positions. I guess I should have examined this closer, but I was looking more for leaks, etc. when inspecting the pickup. I will take it to a local shop, a place where I've had numerous trailer brake controllers installed, and have them fix it up. I guess there are always going to be things wrong with a used vehicle, and it seems this is minor. I know its not the trailer--at least I'm pretty sure--the lights were working fine when I parked it last October. I was just so glad to find a crew cab V-10 with low miles in good condition. I would gladly accept any advice on what might be the culprit regarding the lights. The trucks lights operate properly with the trailer hooked up.
There are separate fuses for the towing lights. The lights on your truck can still work but no trailor lights if they are blown. Try looking at the battery juction box under the hood. I believe it is on the drivers side up close to the firewall and is a black box with designations on top of it. Check fuse F1.9 for trailor tow relay left and right. Also check fuse F1.20 for trailor tow connector 7-pin. You could have a short under the back end there where you were looking.
Check grounds and the fuse. Both were causing the same problems in my F350. The ground was the trailer manufacturers fault since they expected to get a good ground through the g/n hitch. The fuse issue came up once before fixing grounds and once after, so I can not confirm if they are related. My bet would be on the fuse, though.