That was my first guess too, but I checked and made sure Wakeup Scenes were enabled. Still had the problem.
Ok, I see. You might have to start a new game. I don't know about the time skipping with wakeups disabled, but I did replace some code for the wakeup replays since I was using the wrong value to determine which scene will play. That might have impacted some save files? Anyway, if you feel like starting a new game now, I suggest waiting for the full game. It'll be out in mid November.