Never had this issue with previous flocks. They sleep out in the run huddled together and under the 18" that isn't covered (even in the rain). I've tried locking them in the coop for a few days with no change. It's starting to get colder, worried they will freeze to death one night. They have no problem getting food/water in the run or laying eggs in there although the majority of them won't lay eggs in the nesting boxes (which is getting annoying).