I hope to hell it doesn't run Windows. Remember what happened to the Navy cruiser a few years back, when some enlightened person in charge of IT decided to use Windows NT to control the entire ship's systems? When it crashed in the middle of an exercise, the ship was dead in the water... no propulsion, navigation, communications or weapons.
I hope the people making such decisions for the strat will employ something other than Windows, preferably one of the Unix flavors that are time tested and rock solid.