I would make who ever is tuning your truck give it another shot.. Tuning is the key to a happy 5r transmission. Give the guys at Innovative a call and have them take a shot at tuning your transmission.
i sure would hope a built trans would be able to handle a simple tuner. try different tunes maybe but the bottom line is that this type of story is not unheard of when it comes to ATS trannys.Take the tuner off and return it to stock, if your transmission survives, then it's your tuner.
I would bet your tuner is killing your transmission, FWIW...