Do you have the EEPROM enabled? If so... You need to pre-load the default settings into the EEPROM with a M502 and M500 pair. Just because you have a value specified in the Configuration.h files does not mean that value is being used.
You can see the values being used by giving it a M503. It might be good to check and see what Z_PROBE_OFFSET_FROM_EXTRUDER is being used.
You can see the values being used by giving it a M503. It might be good to check and see what Z_PROBE_OFFSET_FROM_EXTRUDER is being used.