I had a problem with my hens cleaning out there nest boxes as well, and couldn't figure out why. My grandfather stopped by on night and fixed the problem for me. He raised the boxes up (as I had them on the floor as well) about 12 inches, and put a small lip on the bottom and a shade over the top to make it dark in there. He also put a wooden egg in each nesting box. They finally figured it out and have left them alone since then and I haven’t had the problem since. I'm not sure what the problem was as we changed all of those things at the same time, but it worked.