This is a long shot, but consider there may be a link between contaminants in your coop and your problem.
Don't clean the coop unless you've got all your birds in another enclosure, far enough away that airborne particulates from your coop won't be inhaled by your birds. Don't just shoo them out into the yard: cage them and put them out of harm's way.
Use bleach and water solution or Oxine or some other trusted germ killer on all the interior surfaces in your coop. Let everything dry before you put new bedding in. Don't rush this step. You need to kill whatever is hurting your flock. If it were me, I might spray and dry, and then spray and dry, just to be sure I haven't missed any cracks or crevices.
Don't put your birds back into their cleaned coop until you're sure everything is dry and all the dust has settled. If you've got a nasty bug, germ, bacteria, fill-in-the-blank-a-cillis in your coop, you're launching it into the air when you clean the old bedding out. Three weeks sounds like it could be the length of time a nasty coop bug needs for incubation.
I hope you find the problem soon.
I had an uncle who claimed that he was responsible for keeping the coop clean. He scraped the poop out with a wide metal spatula every morning. What he failed to recognize was that my aunt sprayed the interior of the coop with bleach and water once a week. He was getting rid of the parts that they could see, but she was getting rid of the bad stuff that they could not see. Both steps were essential to having a clean coop.