How are you checking?
On a piston like that where you can't put your bridge directly over the wrist pin, you need to rotate until the piston is as high in its travel as it can be, then put your bridge on one side of the piston. Push down all the way, record the measurement, then push down all the way on the opposite end of the piston so it will rock up in the other direction, then record your measurement. Average the two and you can see how far down it is.
I wouldn't expect the numbers to be so different on adjacent holes, even on factory blocks that have not been square decked, it will be similar, but you'll see extreme measurements on opposite ends of the decks.