I'm sorry it has taken me so long to look at this. Does your printer still have this problem?
If so, then I can think of a these possible explanations:
The Z motor is consistently skipping steps when moving in one direction, but not when moving in the other direction. To test this, home the printer, position the nozzle at a known height above the bed, then send these commands:
G91 ; relative mode
G1 Z15 F100
G1 Z-15 F100
G1 Z15 F100
G1 Z-15 F100
... (repeat that pair of commands several times)
G90 ; back to absolute
Then check whether the nozzle height above the bed is the same as when you started.
The print head is crashing into the bed before the Z probe triggers, causing missed steps at that point.
The sudden stop that occurs during bed probing is causing the missed steps. To check this, position the head over the bed but above the trigger height and send these two commands repeatedly:
G30 S-1
G1 Z10
G30 S-1
G1 Z10
...
The trigger height reported by the G30 S-1 command should remain the same to within about 0.02mm. Does it?
HTH David