Sounds like they want a dark hidey spot to lay... maybe put up a half curtain to make the nest boxes you want them to lay in more "private" and desirable. I find they like to be "confined" or enclosed in a nest box..... maybe a board to cover the box with a little in/out hole for them to go in/out? so they feel more enclosed? I used a tarp once to make a half curtain and my birds really liked that.... also put fake eggs in the boxes where you want them to lay.
Jess - that could be it. Do I remember correct? Your nest box in your coop is one long open space. Is that right? A chicken sitting in there would feel like they were out in the open. OK... putting my thinking cap on. I picked up free wood today - I'll see if I have some that we could use to fashion individual pop-holes or something.