Holes have a taper

you maybe reaching the tolerance that MDF can hold, while MDF is More Stable than other woods it still changes shape massively compared to metals and some plastics. i will try to run some holes on my phantom s4. it does many small move like your, I suspect I will get the similar results as you. that would mean tool deflection and/or material movement

Well that I hadn't thought of. I'll be very interested in your results.

so i have had trouble holding that close of a tolerance, my holes are strait but the size is +-/0.003 with it tending toweds the small size. i can sneek up on it but not worth it for what we run on the phantom. may stick some wood in the mazak vtc-20 and run blind pocket and probe it