I meant to respond to this the other day - my first though was irritation from the tube - this seems to be especially common in smaller dogs and can last for a pretty long time (2+ weeks doesn't seem too long).
However, it's hard to tell without hearing the sound, and if you think he's at risk for kennel cough (especially if you took him around a lot of other dogs while the vaccination lapsed), it's worth getting it looked at. I think what I would do is wait a day or so, and if it got worse or didn't seem to improve, call the vet.
"My favorite color is green, green like newly cut grass. When it comes to green with envy, though, you can stick it up your @ss!" ~ Grammy