sounds like your truck needs a update. ford will often update the computer in a truck during service. if your tuner is up to date with fords newest programing, but you truck isnt, it could possibly think it has some "aftermarket tune"
I took it to Ford to get "reflashed" and they said that there was no performance mod or chip that has been put in the truck. I paid $100 for the reflash, why wouldnt they at least put the update or make me aware that there is one while they were plugged in?