Megatronics v3.0 on Space Monkey Gorilla. Y axis is skipping steps.

When printion on Marlin it is no issues, but I want to change firmware to Repetier.
I have used Repetier-Firmware configuration tool for version 0.92.9.
When printing Y axis is skipping steps on random layers. When the Y-axis is moving towards zero stepper motor stops for a moment or two to the corner and continues to move in the opposite direction. If you print a rectangular pillar model is shifted to the same side on the axis Y.
I tried to change the stepper motor driver. I tried to change the socket on the Y-axis to extruder 1. The problem remained.



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