I was going to suggest coconut or almond milk as well, but also one that is fortified.
My daughter and I are both lactose intolerant, and any dairy at all in the diet will cause gas and diarrhea. This would definitely be the first place I'd look. Often times what happens is the doctor tells you that they can withstand some dairy, but they leave you to determine just how much that is - there is no test to determine this and it is just by personal experience that a mother has to decide how much to limit the dairy. For example, my daughter could eat hard cheese, which has less lactose, but still to this day has trouble with ice cream and milk. A general rule of thumb is the harder the dairy product, the more lactose in it. They now have lactose free yogurt that is NOT soy, which I was thrilled to find in the dairy section!
My advice to mom is to eliminate ALL dairy for two weeks, see if the symptoms go away and then gradually, one item every two days, add back dairy, starting with hard cheese and see how much he can tolerate.
All of the above, of course, ONLY pertains if he is lactose intolerant. It is a simple blood test, and I would highly recommend he get it if he has not already!
But I am not a doctor, so all of this only comes from my personal experience. Just suggestions!
Just a note - I was raised entirely on soy milk from birth, as was my daughter and both of us are "fine". (although some may argue that point!
)