I thought my DS1 was allergic to dairy as he reacted to yoghurts too. Somehow I discovered that is was only fruit flavoured yoghurt, plain was fine. He was fine with cheese, and when I tried it later, with dairy milk. When he was 2 we discovered that he has a sulphur allergy so all i can think is that when he was under 12 months, even the small amount of sulphur in the dried fruit in the yoghurt was enough for him to react. Now he eats them fine and can even tolerate dried fruits on their own, but I still think this must have been what it was.

I can't see that it's likely he has an allergy or intolerance if he tolerates formula and cows' milk fine, so possibly there is something else he is reacting to or otherwise a big co-incidence.