Do they strictly stay in the run, or do they get some free range time? Your coop/run is nice, but pretty bare. Boredom is often a factor to consider with bad behavior. Consider adding some clutter: https://www.backyardchickens.com/threads/a-cluttered-run.1323792/ to provide hiding spots and something for them to climb up on, and/or piles of dried leaves, yard debris, etc for them to scratch and dig through.