Nozzle scratching build plate

I had the same problem. It was resolved by downgrade firmware to 1.1.0.38. But then I found solution by editing config on newer firmwares:

I compared configs. Problem with leveling was in gcode_macro.cfg in “[gcode_macro G29]“

Old (which works):

  SET_ADJUSTMENTS_FLAG VALUE=1

  G28 Z
  BED_MESH_CLEAR
  Z_TILT_ADJUST
  SET_PIN PIN=fan0 VALUE=127
  M109 S45
  SET_PIN PIN=fan0 VALUE=0
  ZDOWN_SWITCH ENABLE=0
  G28 Z

  SET_ADJUSTMENTS_FLAG VALUE=0

New (with bad offset):

  SET_ADJUSTMENTS_FLAG VALUE=1

  G28 Z
  BED_MESH_CLEAR
  Z_TILT_ADJUST

  SET_ADJUSTMENTS_FLAG VALUE=0

It seems to me, that problem was because of absent: ZDOWN_SWITCH ENABLE=0 and G28 Z.

All way of my research I described here: Z offset not saving - #17 by IgorA