This is just a thought, but do your close neighbors have any chickens where your newer birds could have gotten infected? The wild birds in an area can carry these kinds of diseases between farms easily if a neighbor's chickens have it. Certain diseases like mycoplasma can be transmitted through a hatching egg. About the safest way to get disease-free birds is to get chicks from a hatchery. It seems too often where breeders will sell chicks and pullets who are carrier birds. Some people can be unethical.