I was going to suggest food or ears.. Tucker has bad smelling ears if he is on a food that doesnt agree with him, that is my sign that he needs a different food. When I got him he was on puppy chow and had a terrible ear infection and any time Ive tried him on any kind of food with corn in it his ears starts stinking again. So we stay away from corn. Anyways. Im gald that you found the smell.
I would also suggest changing his food if the smell continues.