I just started a game as the Hansa (version 1.05b), and when I turned protestant, the Papal States and their allies declared war on me. It was a catastrophe; I could get Savoy away easily, France took some territory, but the Papal States just wouldn't let go... the war dragged on for 14 years. Of course, all of Hansa was rebelling by that time, but I saw no problems in the Papal States. Does the computer get additional unrest thanks to a long war, or does it just not show the correct rebel chance when you click on foreign territories?