Of all the theories I've heard or read, Gen. McInerney's seems to be the most likely, given our years of experience with allah's fanatical fanclub.
I wouldn't be at all surprised to learn that the airplane is in a hanger somewhere being painted with another airline's colors/paint scheme in preparation for its intended mission.
In the meantime, it's a nice distraction to keep us from paying attention to what the other hand is doing.
For an excellent reference (and really exciting read), see "By order of the president" by W.E.B. Griffin