It could be an allergy. When my son was about your son's age, he had diapers that sound similar to your son's, and it turned out he was/is allergic to milk and egg. Try cutting dairy totally out of your diet for 7-10 days to see if it helps things at all. It sounds hard, but you can do it. I ended up cutting milk and egg out of my diet for a year. You can also bring a diaper to your doctor and they could check it for traces of blood (another indication of dairy intolerance/allergy), although that is not always foolproof as it did not catch my son's allergy. You may also want to try taking a probiotic (PB 8 is a good brand they sell at Whole Foods). It might help break down any proteins your son may not be able to tolerate -- if the allergy/intolerance thing is the cause.