Hi. Not sure this is exactly your problem, but it kind of looks like the one I and some others had a long time ago. I thought they fixed it with more recent Nomads but you said you had your for a long time before trying anything so maybe there’s something here:
We had issues where the X axis would drift over time. For me it was always to the right - I think this was the case for the others who had this problem as well. So what happens is as your workpiece gets milled out at lower and lower Z values, all of the walls facing towards the -X direction (the right sides of all your holes) drift further and further right as the endmill crashes into the entirety of the wall-previously-cut and shaves away the whole wall by however far it’s drifted since the last pass - meanwhile all the walls facing the +X direction end up stairstep tapered as the endmill drifts away from the wall at each pass.
So for a hole, like yours, you’d expect it to be too large in X, with one of the sides tapered (hard to see from your photo of the two deep holes, but the side view looks like I would expect (the drift would be to the left in that image, so either your drift is reversed or that image is of the back wall, not the front).
Here are the pictures of what my tests looked like so you can see the artifact you could expect from this issue:
If you follow that megathread you can see other people’s issues (ignore the scalloping on the head shape, but the rest were legit I think), and how it got fixed - if this is indeed your problem I think it is an easy fix.
If you want to repeat my test you can use one of your 3x2x1 blocks of wax or Renshape and run it on my test files, here: