Selecting the "Bridging fan speed override" stops all fan on commands from being emitted in the gcode file. Also, a much more minor issue, selecting the blip fan option causes the fan to blip before the zero fan on layer 1 (e.g., the fan should not be blipped when being commanded to go to zero).
This behavior was observed (and diagnosed) on the default Simplify3D configuration file from the Prusa site, for an Original Prusa i3 mk2.
Mark