Not all fans work for the whole control range. One fan I have works from 75 to 255 while another only starts up for values greater than 200. Try setting the minimum fan speed in slic3r to 250 and see if it comes on then. Slicer will only turn the fan on if the layer print time is below the specified threshold. The only thing that will be guaranteed to bring the fan on is bridging.
Using ABSPrusa Mendel Zaphod with Pronterface and slic3r 1.3.0. Printing well with 3mm PLA and ABS through 2 x J Head Mk IV b and Wade Geared Exruders. Controlled using RAMPS1.4 board running Marlin_v1.1.9