The Spanish seemed perfectly healthy when they came to the Americas. The American Indians... well, they were pretty healthy too. But the Spanish had been raised in cities that were poorly sanitised, and lived very close together, so they'd been exposed to a lot of germs. As a result, they were very healthy, with very robust immune systems. They had to be, to stay alive.
The American Indians, on the other hand, were not nearly so close together, and they had a lot more room to be clean in, so there wasn't nearly as much bacteria/virus around them. Thy too were healthy, but didn't have the immune systems to handle what the immune systems of the Spanish dealt with on a daily basis.
Thus, when the two parties met, the germs that barely bothered the Spanish infected the American Indians and wiped out a good many of them.
Replace "Spanish" with "Chickens" in the above story, and "American Indians" with "Quail" and you'll have a pretty similar experience. Chickens have been factory-farmed and barned in unsanitary, damp conditions for many years. The ones that survived had healthy chicks with very strong immune systems that could carry a lot of diseases.
EDT: Of course, if you keep a small, closed, NPIP flock of chickens in sanitary conditions, and the quail also in sanitary conditions, you're not going to have nearly as many problems as someone who brings in chickens from everywhere, has a large flock, and/or has lax standards of cleanliness.
