First, are you sure the coop is fully secure and there's not chance that some sort of vermin isn't disturbing the birds in their nest boxes?
Second, a picture of the boxes would help. Many boxes are deep and dark enough to really be a "preferred location."
Third, are you sure there are no mites in the boxes. Some mites can hibernate for years and then come out and bother the birds as soon as they smell them. Do you dust the boxes with Diatomaceous earth, as it discourages mites.
Once, you've confirmed the above 3, I would then see what happens if you keep the birds locked in for a week to see if they get the idea that nest boxes are the right spot. I have had Ravens fly right into an open coop to steal eggs, I've heard of both squirrels and snakes stealing eggs.
This thread might give you some ideas of nest boxes that chickens like:
https://permies.com/t/171763/Nesting-Boxes-Hens-Big-Put