Intestinal Infection
There are so many things that can cause stomach upset and intestinal problems. Some pets (and people) are more susceptible to these types of problems. Here' some information that might be helpful.
http://avidlifepet.com/inflammatory-bowel-disease-in-dogs/
It might be dermatitis. Here's an article that describes the condition. Sounds like you've already addressed changing the food you are feeding.
http://avidlifepet.com/dog-dermatitis/