I've been having this too, I find if you can leave the game in a window in the background or hiding in the tast bar you don't loose moral or troops and your pop will actually grow. you can leave the game running and not touch it for 8 hours before issues, in which case you need to reboot. I have also found that 6-10 hours without the game loaded is when the proplem appears for me.
it's not a solution but it makes my life easier in game.