Mine were living in my house when I first started putting them in the run. At first they HATED the coop, and would run out of it into the coop. I think they associated it with the adult chickens, who are always mean.
Suddenly the other day I went out and found all of them IN the coop in the middle of the day. I think they realized that during the day the adults are in the run and the coop is a safe place to play. So I put some food up there for them.
They love being in the coop and run, but at night they don't want to go into the coop on their own. It'll be dark and they'll still be in the run screaming bloody murder because it's dark and they want to go into MY house, not the coop. I have to grab ALL the babies and put them in a special hiding spot in the coop and they still scream bloody murder.