I've heard about the "pause bug" as well, and avoid pausing mine for several days unless they are between generations. I'm a little paranoid because I have lost all my games before and had to start over. So, my advice is just wait until the end of a gen and pause before you hit the new gen button. Then even if it doesn't pause for some reason, nobody will die and nothing will change. Make backup copes of your saved game folder too, of course.

Edit: Yeah, what knk said. lol Sorry knk, I didn't see your post.