I had the same issue with last year's chicks, even though they were brooded right outside in the run, in a big wire enclosure in full view of the older birds. I put out multiple feeding and water stations, had more than enough roosts, and a great hidey hole in the form of a huge, hollowed out half log, hollow side down. The Littles and the Tinys learned to use it immediately if they needed to. I kept their pen door open enough to allow them to access their brooder but not wide enough for the Bigs to follow them. I had full integration with the flock by 4 weeks old, and they did great - except!! Yep, loafing in the nest boxes. They started that when they were about 7 weeks old. Drove me batty! And the dumb thing was that they used the roosts very well - when they wanted to.
Part of it was comfort. I'd taken out their brooder pen, which had plenty of good, warm straw in it. Well, so did the nests. So when they needed a little "escape" they'd use the nests. And because they were used to snuggling together, if one went into the nests a few more were sure to follow. When that nest filled up the rest would use the empty ones. <Groan>
They did stop doing that on their own (or because they got tired of me shoving them out) but still insisted on the nests at night. I did all the usual things - roust them out when I'd catch them and put them on the roosts at night, and finally had to resort to closing off the nest boxes. I hung a big piece of landscape fabric in front of the nests after the eggs for the day were gathered, then rolled it up after dark or very early in the morning. Within a week they were roosting regularly and now, a year later, the only time they are in the nests is to lay. I theorize that maybe one chick in the first group got spooked and hid in a box, and others saw her and just joined in, continuing until it became a habit for all of them. That's my story and I'm stickin' to it! Stoopid chickens! This year's chicks have not done the nest box thing - they are content to use the run and the coop and the great outdoors and leave the nests alone. They were raised exactly the same way the first groups were. Sheesh! Who knows why some do silly things and others don't bother?