How long has the puppy had this? My first thought was Giardia a parasite that is hard to detect as the parasite is not found in every stool sample. .. I know first hand that stools are yellowish and STINk as I had it its awful!. Is the puppy lethargic? Weight loss? Hows the appetite? I would go back to your vet and ask that the dog puppy be tested again for this parasite and read this link so you are informed,
http://www.peteducation.com/article.cfm?c=2+2102&aid=739