Has he been seen by a pediatric Gastro Dr.?
Sometimes allergies can take a few hours to manifest themselves, this certainly seems like a type of allergy or food sensitivity however. Yes, the MRI is great for diagnosing issues that involve soft tissues and other issues, it is not just for the brain.
of course you could get a intolerance everytime. There's no fact to say like, oh yes yesterday I had to much milk, probably I'm going to be intolerant soon..
It can happen all the time. But don't worry about it. Nowadays there are so many supplements available. Also there are milk products without lactose, so you should be fine :)