Are you talking about an in bed connector, or the one mounted on the factory reciever hitch?
From what I have seen so far, the one on the reciever hitch is from the factory tow package, and any in bed connectors are added at the same time as the gooseneck hitch. The in bed connector seems to be however the hitch intsaller preferred, with whatever connector he felt like using that day.
On my dad's 01 dually, the in bed connector was wired with a 6 pin connector. This is convenient, giving the truck 4, 6, and 7 pin connectors. All connectors are hooked into the factory 7 wire harnes, and could easily be converted to 7 pin.
On my 06 F350, the in bed connector is a 7 pin connector that the jerkoff spliced in with 6 wire cable. It has the RV conector, but one pin is dead. He also used crimp on splices, and about 6" of electrical tape so that I blew the trailer tow battery charge fuse the first time I used it

Sometime this spring I intend to run a new piece of cable, and heat shrink connectors to re-do the in bed connector.
If you're having problems with an in bed connector, look under the truck on the drivers side of the spare tire. You should be able to see where the wire comes down from the wall of the bed and is spliced into the wiring for the reciever hitch connector. I would look into how they did that and see if you can find the problem.