I have never heard of water fowl getting fowl pox either but I guess it could be it does sort of fit. How did you treat your chickens? I'd try the poultry aid on these places and see if it helps. Maybe try and keep them out of the pond till they are gone so an open sore isn't a place for bacteria to enter in.My first guess would be pox, but I've never seen pox in waterfowl, so check it out.
-Kathy
Thanks K.