have you done postmortum. check wind pipe on dead birds if its full of chese like puss, this is secondry infection, happened to me last year , lost 80% of my young birds. this year I free ranged the young birds once they were old enough and kept them in a large shed at night with good air flow. maintain good hygiene and cull any birds at first sign of any illness.
seperate all your birds if u have the room and treat with availble meds that dissolve in water for the sick and even the ones that are not sick.look on-line to see what meds or vaccines are used to treat your birds and chicks in the future.