Wakeup scenes were unlocked previously, and functioned. I double checked, turned the events on and off again, but still didn't play. Yes, the first time slot is skipped as if an event were playing, but nothing actually happens.
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.