You are not crazy. I've switched tunes 100 times. To and from Westers GMPP to Stock GMPP. Sometimes I go back to stock and I will get only 15 lbs of boost, keep driving, then I'd get 18, then 23. Keycycles affect this as well.
Also I'd go into limp mode, restart the car, and then it wouldn't do it anymore. And I'm pretty sure I'd get more boost than I expected a few times as well when going back to GMPP. It's hard to remember. But the moral of the story is: This car does some f'd up shit when you play with the computer, but eventually it will fix itself, you just gotta drive it.
I have a 2007, I'm on GMPP stock tune. I'm not sure if it's GMPP that has caused these problems since I never played with aftermarket tunes until after I had GMPP.