Since you mentioned being super clean with the coop, thereby significantly reducing the risk of mold growth there, have you given a critical eye to the feed? Old feed can mold. Some signs of moldy feed aren't all that obvious to the average person (someone not looking for it), I mean... when I think of moldy food, I envision a countless eons worth of something unnameable in a covered dish in the back of the fridge... Not so with chicken feed! Some clues to mold in their feed include a musty, earthy odor, or dull, greyish hue to the feed, this is harder to determine with typical ground chicken feed, so knowing what fresh product looks and smells like will go a long way in determining when it's time to get a new bag. Not saying this is your problem, just saying it could be.