Here is a thought.....
Some milling wax is very flexible.
The flutes on a tool can pull, or push the material. Depends on if you are downmilling, or climbmilling.
I may suggest doing the final interal finishing in a counter-clockwise (Anti-clockwise for Euros).
This is downmilling. This will push material away from tool on the X-Y ever-so-slightly due the direction the flutes are working against the material.
* When you cut the final internal spiral inside a unit in a clockwise motion, this is climbmilling. This will try to pull the part towards the tool.
Usually this is an X and Y force (lateral),and not a Z.
Some wax pucks warp pretty easily during milling due to internal stresses in the material. All solid wax has this happen.
Leave a milled wax puck laying around for years, and you will watch it go to egg-shape and bend and twist as it goes up and down temps over the months/years releasing some of this internal stress. It really is a crappy material to mill for thin copings. You literally could watch it move and warp during milling of a large bridge after the surrounding wax has been milled away.
But, Probably this OP has a mill that has been knocked out of calibration of the Z. Why? Who knows.
It is a flimsy machine that also has a hard time holding calibration. There is no other Dental mill quite as flimsy. This mill is the worst out there, by far. Hands down. No comparison.
I had One and spend many many weeks/months try to calibrate One. Got rid of it ASAP. Very frustrating.
Have you tried the Green wax from Machinablewax.com ? NOT the BLue!! Blue looks pretty, but sucks for milling Dental. Too sticky and soft/flexible. It is good for large, thick objects for casting in foundary. It melts faster, cleaner, and at lower temps for burn-out in Gypsum investments that cannot go up to 1500F. We really don't have this issue as most of us use high-heat investment. This Blue from machinable wax may be different from other sources of wax, but it seems many companys are selling the CNC waxes are getting it from same place?
Scotty