great response. I've done 4 sets of chicks raised by a mama hen now. She sets, hatches and raises them all in the coop/run with the rest of the flock. It's great, easy and fun to watch (bit of a lower hatch and survival rate than incubating). The transition period of mama weaning the chicks and them finding their place in the flock, has always led me to nest sleepers/poopers. Which is terribly annoying. The cockerels seem to be the worst offenders. You're right, the roost without mom is intimidating, and they all feel the most secure huddled together in a nesting box.
I've had to train them by going out every night and placing them on a roost. I have added a 'chick roost', which is smaller and lower than the others and kind of off where the big chickens can't peck them. It takes a long time and is annoying as hell. I don't even know if 'training' them makes a difference, or if they just mature over time to where they're more comfortable roosting with the rest of the flock.
Just when I get everyone roosting on the bars, mama hen and I both get baby fever and we do it all over again!