I am having this problem right now, too. My coop and run are pretty secure, it has 1/4" square wire on all sides and there are no holes under the walls/fence. There is only one spot on the run that has 1"x2" wire on the roof. So what ever it is must go up the 4ft fence to get in, and the nesting boxes about 3 ft off the ground and my hens have to jump to get in. I feel like it may be rats, I know that we have those. And I know they eat anything. My friend had a pet rat that ate her entire cockatiel including feathers, bones. The only think it didn't eat was the skull. I don't know how a snake could get in the nesting box...I am going to put the camera out there and a light to try to catch the culprit....