Yes, I am positive it is in the motors. I removed all three. These are direct driving some ground ball screws. I am going to try to up my frequency to 35,000. It is kind of puzzling that all three started doing this at the same time. Swapping to the gecko's eliminated the drives. I have tried the active high/low settings. I have changed the two pulse US timing settings in motor tuning. I did cut out my first part on this yesterday and it came out perfect size. Clean cuts, but I think it could be even cleaner without the thunking. I am pretty sure is actually stopping in those points for an instant. Otherwise, how would it make noise?
Thanks so far. It seems like it should be an easy thing to figure out, just haven't run into this before.
Here are a couple images of the mill.
I have done a little more work to it. I added way covers and I am adding an aluminum tray to catch the coolant.
I pulled the chain drive off the front and installed the Y motor direct drive like the other two. I get very nice smooth action except for the thunking.