I have never heard of a drone running anything other than an RTOS. However the ground stations for command/control/monitoring are typically run on traditional Windows-OS machines.
The level of performance needed in the GCS is even less than you might think, too -- for most of the UAVs, you don't have direct flight controls -- it's more like a naval ship, where you instruct it to go to certain altitude and fly a flight path you plot on a map. Some of them have more stick/rudder style controls, mainly for landings, which are often controlled by another operator physically at the launch/recovery site (and who might be a contractor vs. soldier/airman).
