I have suggestions....we've battled chronic gut problems in our home and we've completely changed the situation with only a few minor supplements.
1. Digestive enzymes. Get a broad spectrum digestive enzyme and have him take it with every meal. We've been using this one since DS was 3, so it is safe for his age. You can also empty out the capsule shake it with juice if your DC doesn't take pills yet....that's what we still have to do for our 7 YO DS.
http://kirkmanlabs.com/ProductKirkman/283/1/Enzym-Complete-DPP-IVand/
2. GSE - Grapefruit seed extract. It will help combat yeast/fungus in the gut that has destroyed the lining of the gut wall. You can also find this in liquid form if need be. Only a couple drops per day is needed.
http://www.amazon.com/Grapefruit-Seed-Extract-Maximum-Strength-250mg/dp/B002QP9FAS
3. Some form of supergreens....ie., bluegreen algae, spirulina, wheat grass, barley grass. You need something here to help raise his Ph levels so that the body can be in balance again. Here is what I would suggest. Put a scoop of Green Vibrance in juice once per day and ask him to drink it. It's not that bad.
http://www.amazon.com/Green-Vibrance-Kilo-35-27-Ounces/dp/B0054RQDCS/ref=sr_1_6?s=hpc&ie=UTF8&qid=1323785793&sr=1-6
After making these changes in my children's diets, we've eliminated any/all gut problems. I hope this helps. Good luck, op!!