Oh my heavens, are we ever having a huge problem with the flies here in North Peoria. My kitchen was spotless and I still had them inside. They are swarming my backyard en-mass, too. Everyone I've talked to is having major issues this year, even if they don't keep chickens. The fertilizer we used in the garden and the chicken poop is attracting them more so than normal versus some of the others people, but you can only clean up so much of that. My coop and yard don't smell at all, but you can see the buggers all over.
Once my work on the new coop is finished today, I'm making a couple of fly traps to hopefully help get rid of them. A simple funnel and a glass mason jar with the ring should work wonders for it.
Am really glad to hear we are not the only ones. Ugh, I thought it was due to our new additions (chicken tractor and composter) to our back yard this year since we brought chickens into our lives. My husband is a freak about flies. Can't stand them. Won't eat "alfresco" ever. Gets obsessed if one is in the house and just has to get rid of it or he can't concentrate on anything else. We are in NW Phx by Ben Avery. Even with great breezes the flies are ridiculous and our yard and tractor are quite clean. I had seen something on youtube where someone made a flycatcher and then fed the flies back to the chickens. Thought I might give that a try.