I havent seen any surprises like that. When I do an estimate I try to remember to print out of at least the Tax Summary (if not a draft of the 1040), so you have something to refer back to in case it looks totally different than you remember.
Theres also a new feature I saw (maybe its not new, I just never noticed it before?) its Auto Calculation, maybe you dont have that turned on, so it didnt auto calculate when you first did the return, and the calculation happened once you saved and exited the return only to be discovered once you opened it back up? Ive got it turned on, so it calculates as I go.