Ah, okay, so these settings are just for the X driver? What about the Y and Z?
Just to follow up on this, the issue wasn't anything software related. It was purely EM/RF interference from having the 48v power supply for the stepper motors in the same box as the breakout board and stepper controllers.
I pulled out the power supply and put it in its own box on the other side of a wall, and there are no more lost steps.
Did you have shield wires to the motors?
Shielded only at the ground in box
Sent from my HTC EVARE_UL using Tapatalk 2
All the wires are shielded.