Ok, I'm having the same problem. I'm using v.05. I shut the game off (with out pausing) each night around 10pm before I go to bed and I don't turn it back on until about 5-6pm the next day. Still have people exhausted. I'm not reversing day/night.
When it's mentioned to "put them to bed", does this mean what I'm doing (shutting the game off at night) or to literally drag and drop them on a bed till they go to sleep and then shut the game off? That maybe the step I'm missing.