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