That's great that you have 5 windows - are they closed since it's wintertime or do you have them opened up all the time?
If the vet suspects the cause of her barking is from ammonia, you don't have enough air flow in your coop to remove that from the overnight droppings. No dampness does not mean there are no ammonia fumes.
http://www.backyardchickens.com/a/c...-go-out-there-and-cut-more-holes-in-your-coop
Putting your location in your profile also helps, it gives us a general idea of what part of the world you live in.
I'm glad you were able to seek vet care, what type of antibiotics did she give you?