TJ has the same problem (IBD). He has a very sensitive stomach. I just changed their food to IVD Potato and Duck. (Under the Vets Instructions). B/C TJ probably has a food allergy or is eating things around the house that bother his digestive track, plus he eats poop.
Here are some good sites that I found:
http://www.vetinfo4dogs.com/dibd.html http://www.marvistavet.com/html/food_allergies.html http://www.acacanines.com/inflammatory_bowel.htm
I hope your baby gets better soon!