First, what Z axis do you have, Belt driven, Z plus, or HDZ? So it seems that the further the Z axis travels the further off the actual distance is:
.125 = 0
.25 = .03
.375 = .071
.5 = .093
.625 = .097
.75= .116
I would lean toward that you need to calibrate for belt stretch. Of course it’s weird that this would start with the BitZero V2, belt calibration shouldn’t be effected by the zeroing method.
So two other questions:
What happens when you use the BitZero for X, Y, Z zeroing on the same stock but just jog the machine instead of cutting? If you carefully jog from the top of the stock going down the measured stock thickness does your end mill sit just above the spoilboard or do you have to stop at .625" because the end mill is at .722"?
Also what happens if you manually zero with just a sheet of paper and run the job again, do you have the same problem?