If anyanomalous behaviors in the movement of the axes, translation type systematic at some point in the press in one direction, it could be wrong values ​​of the backlash of the offending axis.
This situation could occur after an automatic calibration in which backlash values ​​other than 0.
The backlash guards compensate for the play that could occur between pulley and belt over time. These are generally very low values ​​and, when they are activated, you have to do counter tests to see if the values ​​are right.

To deactivate the backlash and then restore the correct functioning if there are really no backlashes to compensate, just give the following commands from GCODE in MANULE CONTROL:
M810 X0 Y0 Z0
M500

At this point perform Z0 and flatness again.