I just went back to test 0.08.1 and everything was fine. Not even the disabled wakeups time skip you mentioned happened. You're on version 0.08.1 and didn't mess with the code at all right?
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.