I'm having exactly the same problems. Oddly enough, when I was playing the old version of the game, I didn't have an energy problem at all ... I just left them over night, and they woke up almost fully energised. Now, I'm lucky if I get a half-full energy bar after having left them over night. I find it very odd that a version that was supposed to fix a fault actually created that fault for me!
That's really odd.
Maybe you should praise them a couple of times for going to bed and like with RL kids, settle into a routine. I play my families from my time morning to about 10, 11-ish before they start getting tired or exhausted.
After that I shut down the game and by the next morning they'll fully (or almost fully) refreshed.