I am curious if it might be an allergy. Did you change feeds recently? If not, I would try changing feeds to something with a different formulation.
Another thought is kefir - homemade, not store bought. Kefir is very much like yogurt, but contains beneficial yeasts as well as beneficial bacterias. A good homemade kefir contains something like 40-60 different strains of beneficial strains as opposed to 4 or 5 in most organic yogurts. The beneficial yeasts will compete with the nasty yeasts (fungus, bacteria, etc.) and after feeding the kefir for a while, should overwhelm the bad and restore a natural balance. Kefir is easily made on the countertop at home and once they try it, chickens love it! It is excellent for people and dogs, too.