If I remember correctly, I posted during the beta about a town that intermittently would show the 15% unrest penalty for not being connected when it was indeed connected, and had not been showing the penalty the turn before. After another turn or two the unrest penalty would go away, only to return again later for another turn or two. Whenever I saved and reloaded the game, the problem would go away.
So I think that this is a real bug, but I would expect it to be very difficult to prove it or fix it, since it's intermittent, goes away by itself, and can't be demonstrated with a saved game.
