Your boxes are being slept in at night. When birds sleep in a nest box, it obviously makes it unsuitable for eggs! You can block off all of the nest boxes at night, and open them up every morning. It should take a few days, and up to several weeks to train the birds to sleep on the perches, instead of in the boxes. How big are your coops? How many linear feet of perches do you have? Are the perches placed ABOVE the height of the nest boxes? Are the perches high enough that birds on the floor of the coop can't reach the toes of the birds on the perches? All of these issues are important, because if your coop is not suitable for the needs of a chicken, the flock will NEVER work well in your coop. Pullets sleep in nest boxes often because they are being bullied by the older birds. Sometimes crowding, improper coop and run set up can cause increased issues with bullying. Perches must be above the height of the nest boxes, high enough that the birds can perch without getting picked on from below or from an adjacent perch. Far enough from the back wall of the coop so their feathers don't touch that wall. Far enough below the ceiling of the coop so that winter condensation from their respiration does not freeze on the ceiling and create a moisture/ice issue that will lead to frost bite. The birds need at least 10 linear inches of perch space per bird. Enough room to be able to fly up and down, or if in a small coop, several access areas where they can step up and down. Birds need a long run way to be able to fly down off a perch without crashing into the wall in front of them.
