With the Predator, it was more or less a flight- vs ground-software distinction, as my sibling commenter says. But even with the inflight entertainment system, where everything's in flight, there are separate computer systems (meaning, CPU's, software loads, operating systems, power busses, communications networks, air supplies for cooling - the whole nine yards) for the flight critical software (flight-critical meaning that an error or malfunction could cause the plane to be unable to fly) and the in-flight entertainment center or any other system of lesser criticality.
Even with UAV's, it's not just a flight-vs-ground distinction either. For example, any drone that's being used for reconnaissance is going to keep a big imagery database on board, simply because there's not enough satellite bandwidth to stream lots of data back to the ground while it's on the air. That server could be running Unix or Windows or whatever, and probably is, because the UAV designers will have gone to a lot of trouble to make sure it can't interfere with any flight critical software.
Even with UAV's, it's not just a flight-vs-ground distinction either. For example, any drone that's being used for reconnaissance is going to keep a big imagery database on board, simply because there's not enough satellite bandwidth to stream lots of data back to the ground while it's on the air. That server could be running Unix or Windows or whatever, and probably is, because the UAV designers will have gone to a lot of trouble to make sure it can't interfere with any flight critical software.