There is general agreement on a few forums that the GMPP tune updates several tables that are not accessible via HPtuners and thus don't get rewritten once installed. I've read that these hidden tables hurt later non GM tunes, as the base tables are better for HPT tunes.
I tend to believe at least the extra tables part of this because the GMPP file size is almost twice as big as other tune files. On the other hand, any tables built based on higher hp and torque would seem like a better starting point for further upgrades than the base tables.
Anyone have some experience with this?