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So, in summary, 3-axis machine - a DIY conversion of a mill. 3 motors, driven by three stepper-drivers, driven by a KK01 BoB, which in turn is driven by, what we understand to be a legitimate UC100. Software : Mach3 and UCCNC with the same observed behaviour.
I don't recall what stepper drivers you are using, or your main stepper PSU.
Observered behaviour: Missing steps (to the point where an axis will halt completely) in a given direction. This impacts typically at any time one axis, but that axis can differ on different tests?
Can you confirm: When an axis freezes - can you jog another axis whilst frozen? (so, if holding cursor-up freezes on Y+/Y-... does pressing cursor-left/right allow X to move)? (my reasoning... under the failure condition, does this only affect one axis or are other axis not currently active/observed also affected)