Does she bark if you are outside, not with the chickens and she is still in her pen? It may just be the fact she is separated from you and is letting you know she doesn't appreciate it. I would work on it the same way you would if you were crating the pup in the house and they fuss. If the pup is barking, ignore it. Reward it when it's quiet (treats or attention .. let her know when she is doing right).
Xan Varik von Fernheim (born 4/3/13)