You have done quite the job making sure the run is the best environment it can be for them that your observation could be correct. How often do you let them out into the full yard? What portions of the yard do they favor when let out? Maybe there is some environmental modification you could do in the yard as well. Focusing on the areas they frequent the most.I know this observation is the opposite of popular opinion, but every time the hens are confined to their run, they do much better than they do with free ranging in their day.
More poops than usual and they're more thoroughly digested than usual. Weight gains. Cheerful attitudes.
Maybe the forage in my backyard (what there is of it) is unhealthy? Katie has got her energy back in full and her comb is turning red. Mary and Peggy look like a pair of feathered happy buddhas. Melissa doesn't let being in the run stop her from chasing pigeons or hopping up on things.
The difference is clear and almost immediate.