Perhaps run the tranny in manual mode with a load on and see if you can duplicate the sound at will, then take it to the dealer. All of my Allisons at times have shifted rough. They used to say right in the owners manual that the tranny is not the same as the light duty tranny you may be used to. Its a HD tranny that at times acts like a HD tranny (stiffer upshifts and downshifts). I don't know if that is still in the owners manuals of the newer trucks. I have experienced similar responses in my DAs but its hard to know if yours are more pronounced than they should be or if your just not used to how these tranny's work.