Do you have the EEPROM turned on in your version of Marlin? If so, what ever Z_PROBE_OFFSET_FROM_EXTRUDER that you set will be ignored. It will pick up the stored value in the EEPROM. Probably you should turn off the EEPROM and EEPROM chit chat until you get the Z_PROBE_OFFSET_FROM_EXTRUDER dialed in and at the right height.

If you can't do that (turn off the EEPROM), you can do a M502 followed by a M500 to load the Configuration.h settings and then store them in the EEPROM.

But before you do that... Do a M503 and see what it says the Z_PROBE_OFFSET is. Probably, that is where the bad number is coming from.