Look at it this way: USAF SPACECOM wanted to build their own shuttle fleet, and decided, in a cost-cutting move, to not bother. But there are times when it'd be nice to go up in a shuttle in support of military objectives, so they rent the time from NASA and use their own crews and don't tell anyone what they do.
I have some guesses, but they'd be just that; and if I knew, it wouldn't, um, be proper to say, now would it?
Anyway, your imagination is probably more interesting than the truth.