Food allergies and intolerances can start so small as to not be noticeable until later when there is gut damage and then the symptoms can become much more pronounced, either gradually or relatively suddenly.
It may be lactose, or if there is dairy in the milk in general, it could be a dairy intolerance (which is usually to the milk proteins, like casein, than the lactose itself).
The only way to really know for sure is to try a completely dairy-free milk. The downside of that is that often those are soy-based, and soy protein is similar enough to milk protein that if your LO is sensitive to one he may react to the other as well.
I'm not really familiar with the different milks/formulas out there now as mine are quite a bit older, plus I'm in the States (I'm guessing you're in Britain?) so I"ll defer to others as to what milks might have which substances in them.