anything that would do that within the engine would probably cause a CEL.
to check the tune, open the tune with your EFI Live program and click [+] to expand the "EFILive custom calibrations". click on each one of the DSP programs to reveal the tables. if this is beyond you then i suggest going back to ATP truck performance or Rob to have them go over it.
i am also wandering if the tune was not made very aggressive to protect a stock transmission. the Edge programmer on the higher settings are not transmission safe. it will run strong but not for long
Jason