Is there a medical reason you're not breastfeeding? Don't mean to be personal, but breast milk is the only food that gives an infant the first immune resistance and digestive capability. You can't reproduce this with formula. If you must use formula, then it appears you need to test your child for food intolerances and allergies, as soy is also a common allergen, thought dairy is the worst with wheat second. This happens most often when the immune system is overactive, and one way it gets that way is if the child was given antibiotics and the lack of the colostrum in your first batch of breast milk, because infants don't have much of an immune system yet. If you can't breast feed, given this problem, discuss with your doctor giving the child probiotics that focus on digestion, particularly one I believe is called bifidus infantus. These are friendly bacteria that live in the intestinal tract and ensure proper digestion. You might also discuss supplementing with colostrum. Good luck.
Not sure of the base, but he could have a cow milk alergy. What about a soy based product?