I guess your issue is coming from the belt or pulley from the axis 3.
What changed from 2.0.0 to 2.1.0 (Raspberry Pi image):
– Torque on axis 2 stays ON during all calibration (in case the torsion spring makes the arm lean forward)
– Speed on axis 3 during calibration is reduced a little bit, but the torque stays the same.
So, what happened here is (my guess): your axis 3 belt is not tensed enough, but just at the limit so that when the speed is increased a bit, the calibration will still be done. The axis 2 should not have a problem, I think it’s already correctly tensed.