At a guess you have the eeprom enabled and have not updated that
If you use M500 even once then from that point on you must update setting with further M500's.
Once the eeprom is used the setting in the firmware are no longer used being superseded by what is in the eeprom
reset eeprom to firmware by M502 then M500
If you use M500 even once then from that point on you must update setting with further M500's.
Once the eeprom is used the setting in the firmware are no longer used being superseded by what is in the eeprom
reset eeprom to firmware by M502 then M500