I have this problem too. I notice it only in 5th or 6th gear with heavy throttle, but I can't duplicate it in lower gears, or at lower speeds. Most of the time I notice it getting on the freeway, it feels like hitting little bumps, but really its the truck stumbling, missing or cutting out. It does it with the comp off, but not nearly as bad as when the comp is on. I do think it is cold weather related. I think it is a software issue in fuel mapping or something. I think that load or speed has an effect on it since I can't duplicate at low speeds. Maybe we need marco and that Catcher to fix this.
Lets get some input from everyone that has this issue and find a fix for it.