Ive already encountered a bug whereby I did a comparison copy all over to my tune from another, and found the injector offsets scanned differently (retrieved in seconds versus base tune was in ms) from my current car and so the copy over from the other tune caused my injector offsets to be off by 4 decimal places. I would suggest opening each tune in two windows and comparing your base/copied tune versus your new tune's injector settings, make sure it all copied over ok.