FWIW, there's a lot we don't know - but are learning - about bacteria and the gut. For example, if I'm not mistaken, a baby gets a lot of important gut bacteria from it's mum through breastfeeding.

So when I hear all this argument about raw vs pasteurised milk, I expect there really is something of health benefit to raw milk, just there's a big downside of harmful pathogens that can be cured with pasteurization. That doesn't mean all raw milk is unsafe. Like with raw eggs in the UK, or not iodizing your vegetables, it can be safer with care over production.

Anyway, that is to say, I figure there could be some interaction with the bacteria in the raw milk helping your son to digest it.

But having seen the other comment suggesting homogenisation, that sounds more likely to me. (Just a guess though.)