Make sure you've set the minimum percentage of the fan speed so that it can spin up to rev. Use 50% as minimum for example. If auto fan control is on the fan speed depends on layer times. See the cooling section of slic3r. If the print layer time is much longer it may be that the fan speed is off or too low. Depending on the print, at the end the layer time may drop down within the range set in cooler settings, at which point the fan starts spinning.