You didn't mention how many of your villagers are farmers. I've discovered that when you're "offline" the villagers only do what they're trained to do, or so it seems, so farmers will farm, builders build, and scientists research (as best I can tell). And if they're old enough to breed, and know how, you may come back to a baby or three.

I don't think it's a flaw that they don't work faster at 2x. As far as I can tell the speed is just relating to real time. At double time, one hour of real time is one year of game time (based on nursing taking 2 years/120 minutes).

If I understand correctly:

at 2x one hour real time = 1 year game time
at 1x one hour real time = 6 months game time
at 1/2 x one hour real time = 3 months game time

Of course I could have this totally backwards? I am such a Luddite.

Don't know if that helps you figure out how to proceed - you could just pause the game when you exit so nothing happens until you restart a few hours later? Good luck.

Dar