If it goes inside it should be disabled by
<p class="p1"> if(pwm_pos_set[PWM_FAN_THERMO] == pwm_count_cooler && pwm_pos_set[PWM_FAN_THERMO] != COOLER_PWM_MASK) WRITE(FAN_THERMO_PIN,0);</p><p class="p1">in HAL.cpp.
</p><p class="p1">
</p><p class="p1">Possible reasons are if FAN_THERMO_PIN has a pin number that is also used by an other pwm signal or if it is not the pin number where the fan is connected.</p><p class="p1">Just my first ideas to look for.</p><p class="p1">
</p>