It sounds like something acidic. Does he eat a lot of apples or dried fruit?

I would reduce the amount of fruit he eats and try and get him to eat more meat and bread or cereal or rice or pasta...things that will bulk it out a bit.

Otherwise, does he eat a lot of dairy? Maybe he is allergic to the lactose enzyme in cows milk...it would make sense if you have been supplementing the breastfeeds with cows milk.

Good luck!