Have you checked to be sure the crate is the right size? If it's too small or too big, they might feel intimidated. One thing I did with my dogs was put one of my shirts or blankets I slept with in the crate. This added comfort but also let them smell me in the crate. I also keep the room with the dog crate in it calm, and quiet. I have found that if it's calm around the crate, my dog is calmer.
