Are you checking the deck heights in the center of the pistons or on the cam and outside block edges? Are you rocking the pistons in the bores and averaging the differences to get your readings?
Lots of variables in the ways to get those measurements
I use a thin bladed screwdriver to move the pistons in the bores, front to back and left to right and then average for the centers
I used the highest readings on the piston tops to the head contact distances to set that clearance, better to be safe than sorry