She may have an infected oil gland. It can happen. Here is an article from Majestic about that. http://www.majesticwaterfowl.org/mmissue71.htm
Do you think maybe the meds she is on could be causing the issue with her feathers? when you put her in water does she start bathing and preening afterwards?
Maybe the meds are making her feel sick and she's not preening, and that's just a guess.
-Kathy
Thanks so much for the responses. I don't know what to do now, and I'm very worried about this. I just heard from Kim at Majestic, and what she said has me second guessing my vet. She isn't a fan of doxy and said it's very hard on ducks and that most vets she knows of would have opted for Baytril. I was already worried about the doxy because I know it's hard on humans, and it makes no sense to me that this duck is worse after a week of meds than she was when we took her in. Would it be irresponsible of me to go against the vet's advice and switch her to Baytril? I absolutely cannot deal with losing another duck right now even though this one isn't a keeper.