Persistent cough after being given antibiotics for kennel cough?

My 1 year old aussie was boarded for a weekend 3 weeks ago. When we picked her up, she seemed perfectly fine, but after a couple days she started coughing like she had kennel cough. I took her to the vet where they said she did indeed have it, and gave antibiotics. she has two more pills left to take, but keeps coughing when she gets excited/goes to bark. she has seemed fine in every other way- wants to play, eats, drinks, seems happy. today she threw up and seems a like her tummy is upset, but I'm not sure if that has anything to do with the kennel cough/antibiotics. has anyone had anything similar happen? can kennel cough persist after antibiotics are taken? the vet didn't seem worried at all when we took her last time.