I will explain this to everyone why it does this.
The 5R55E transmission has an adaptive learning strategy. In other words, the ECU learns your driving style and adjusts the transmission fluid pressures accordingly.
IMO, that is one of the negative things about the Trac and I personally feel that is part of the reason that some of the problems some members have.
When you are running a chip, XCal 1, XCal 2, Or XCal 3 the computer is trying to lower tranny pressures. At the same time, the reprogramming in the ECU is keeping the pressures higher.
Essentially, we are having a power struggle. When one of the "powers that be" "leaves", i.e. the Programmer, the learning strategy makes it shift like crap because it has tried to lower the pressures as low as it can possibly lower them.
When you unplug the battery, it will put the pressures back to the default setting before it starts to adjust for your driving style.
It will learn in time if you leave it alone, but you can be causing wear on your clutches and excess heat. Best thing to do is ALWAYS disconnect the battery after going back to stock.
Tom