mbam,
This is complicated, so no one else may be able to explain this in detail. We'll give it a shot.
Backlash does apply to Hand Wheel's in position / increment mode. Not in free wheeling Tach mode.
It also does know "how much" and "if to" add/subtract steps in stepper mode on the first move. Click on the button to the left of the white BACKLASH box in CNC SETUP under DESTINATION CONTROL. This will explain how it does this using positive or negative values entered into these boxes to tell it which way the first move would be travel after homing.
What is most likely happening in your case is complicated because you have encoders that report Z axis positions in the readout displays using a different number of encoder counts per inch (per rev) than the number of micro steps the same axis motor uses to move 1 inch. The display reading you see Z.0112 is directly related to the values from the encoders, which may not match up with the step count. The G code program Z.01 dictates the number of steps to move. There maybe another variable applying itself too. You're Z dimension is close a(0.0012) nd maybe showing Z differently than X,Y because of gravity. The physical head maybe in a little different position than the stepper motor positioned it at.
See (Closed loop position correcting Steppers) by clicking on the button to the left of SERVO-STEP box under GENERAL SETTINGS in CNC SETUP.
You may have to adjust , test and re-adjust the Z values for both step count under RATIOZ and encoders per inch under AUX ENCODER SETTINGS, plus figure in that the BACKLASH value, may or may not get added to this. If this were a Closed Servo it would self correct to the Z readout display automatically. Reading the encoder position of Z , 12,000,000 times a second. Steppers can position, but they go to fixed positions units based on (steps per inch). Unless the encoders report they are out of tolerance, they will not remove the difference of 0.0012, where servos would strive to do position error correction to +/- 1 encoder count accuracy despite the tolerance you've entered.
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