When a dog has diarrhea, the stool can turn yellow. Yellow stool means that the stool is traveling very quickly through the small intestine. When a dog has diarrhea and it's yellow, it can also mean that he is eating foods that he can't tolerate; so the dog's food should be changed.
If your dog is a puppy and is eliminating yellow poop, you need to take it to the vet. If a puppy drinks too much milk, this can turn his stool yellow. Puppies can easily be killed by an infection, so treatment must begin ASAP.[LEFT]
Read more: What Causes Yellow Stool in Dogs? | eHow
Maybe try a different vet, get a 2nd opinion? Switching foods on a young puppy is very dangerous, it causes digestive problems & that causes them not to want to eat which ultimately gives them hypoglycemia. Hope he'll be ok!