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Having some similar trouble- random missed Z moves on cuts that prevent me from doing anything useful with the machine.
With the z anti backlash nut backed all the way off, accel turned down to 35 and max speed turned down to 7 I got it to work reliably with the Z torture test. Might be able to handle more than 7, I was just getting frustrated and went very conservative.
With the anti backlash nut in place (not very tight, hanging halfway out of the nut trap) it still binds and buzzes like crazy. Have adjusted vrefs ranging from .4-.9 without much affect.
I think maybe the rigid coupler is part of the problem. The first one I printed was way off center, and the one I just redid in an attempt to fix this might still be a little off. I can feel sometimes it is slightly harder to turn the z screw for a little bit.