If you didn't flash the tune that would cause it, another case of not following the instructions haha, I saw on myg37 there was a guy who just did the same thing, except he burned up one transmission, replaced it with another transmission, damaged that transmission, swapped in a new stock valvebody, then finally got around to tuning it after throwing out the gtm valvebody
Edit: if only he had put the gtm valve body in and then tuned it.