My good friend Bill Stockard, TDR contributing editor, who knows infinitely more than I do about these trucks told me, after listening to my noisy '06, that he thinks either the ECM is programmed differently or some error is causing one or more of the fuel injection events per combustion cycle that is present in some of the earlier models to be missing from my '06. His advice was "drive it. " That's what I'm doing. At 128k miles, many of those miles working hard, it continues to run fine. I don't hear the clatter when I'm in the cab and it doesn't seem to hurt a thing. I didn't worry about the rattle and clatter of the '01 so don't see any reason to worry about it in the '06 either.
Harvey