M.,
It sounds like your son has a cow's milk intolerance or sensitivity.
My 13 month old son is in the same boat: was fine with milk-based formula, cheese, and butter, but give him straight cow's milk and he screams, arches his back, and sporadically vomits. (Oddly, yogurt and ice cream also bother my son.)
My parents gave him lactose-free cow's milk thinking lactose was the issue, but he broke out in hives all over his torso.
We give him goat's milk and he does just fine. Cow's milk is actually VERY hard for many people to digest, and nature made it with baby cows in mind, not little boys. ;-) I know some Rainbows and Cubs carry goat's milk, as does Lund's. We buy it at the co-op because it's cheapest there ($3.60/quart). If you are enrolled in WIC, they do give vouchers for goat's milk, you just have to ask for them.
Also, I see you're in Hugo. There is a goat farm in Scandia--Poplar Hills. You can buy milk directly from them for very cheap. We are planning to do that, just haven't gotten around to it.
If you go to the co-ops or Whole Foods, you will see all kinds of "milks": soy, rice, almond, hemp.