I went back to the dealer that had installed the original tune. Told them what I had done and the resulting chucking. They were not at all surprised and said they had seen this before. They suggested it had something to do with turbo tables. My driving experience tells me this is the case as I could make the chucking come and go with slight preasure on the skinny pedal.
They removed the new tune and reinstalled the original. Chucking is gone. I pulled trailer lots and there is no chucking. There is something about the engine side of that tune that is not compatible with my truck I believe even though the same tune might be fine it other trucks.