We went back to the vet yesterday and she gave him some different antihistamines to take for the next 2 weeks and see how he is then. She says it is not kennel cough and maybe the windpipe, but to try this first. The whole 30 minutes at the vet's he never coughed, silly dog. Went home gave him the antihistamine and all was great until 3am this morning, he started coughing again for about 20 minutes then all is back to good again. Gave him the morning pill so we just have to wait and see. Thanks for the responses.