I don't know if you are still having this issue, or even playing this game anymore. However I recently went through this and it turned out that it was caused by my time control mod. Rather than just pausing the clock it stopped everything from registering the passage of time. Destructables and such still worked because they weren't ties to the games time, but everything else (aka living things) stopped functioning. So this might be a good place to start if you or anyone else is having this issue.