The weak link in your manure management might be the bedding. I found that straw was not good bedding. Manure on pine shavings dries up faster. Straw bedding just gets soggy and matted. You might try switching and seeing if that helps.
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I recently ran into the same problem, bombarded with flies in the coop. Well we've had quite a bit of rain & i only found out reading on this board that hay/straw expecially when wet/damp/moist is a breeding ground for flies! I quickly got rid of ALL hay on the floor. There is only enuff for there nests/bedding which stays high & dry. Also keeping the poop out daily or covered & dry has helped tremendously in only 3 days. They have an all sand/grit floor so the poop dries quickly & is easily scoopable to remove!