I'm not sure if you understood the fans right.
Extruders can have 2 fans
1. Extruder cooler fan connected to extruder cooler pin, which is controlled only by firmware and turns on if extruder gets warm. Reason is that many new extruders need active cooling to keep melting zone small.
2. Material cooler fan which is connected to FAN_PIN and can be set from host or with M106/M107.
In addition EXT0_EXTRUDER_COOLER_SPEED gets stored in eeprom, which overrides your config settings, so please check that as well if you did not mix the 2 fan functions.