So I have spent all weekend and this week so far on this problem to no avail.
Had one guy on Fusion forum take a look but he could only simulate it so did not see the problem.

I just noticed on the operation I am running now it looked like it dropped a step.
Wondering if I am taking to much of a DOC or pushing too hard on the feed and it is pulling the bit?
Over time it would result it multiple height differences which I am sort of seeing but some heights are correct.

Once this operation is done ill touch off from the top of my stock and see where it thinks it is.