Try putting them IN the coop at night. After a few times they learn it's better to sleep in it than on top of it. I thought my run was secure too so i let them sleep on the roof at night and an owl got one of my roos. It had netting but i guess it was close enough to give it access to the it.If I have young chickens outside, I have put some rice socks out with them to curl up to get some heat. Warm it up in the microwave and it is warm for a good while. I don't really worry about it though since the majority of my chickens seem to prefer to sleep ON the coops rather than in them. Even this morning when I went to check on them, I saw a third of them still outside. Good thing their run is secure enough that I haven't had problems with this arrangement. Dummies leave one completely empty and only one or two in another one. SMH!!!