C.G.
Are you seeing an allergist or a family doc? I ask because allergies in kids are very puzzling/difficult to diagnose. If at all possible see a specialist. My son had allergy issues with milk as well and seeing a specialist made all the difference (or also maybe get a second opinion, you may fidn new information).
Barring that, make sure you are eliminating all sources of milk. There are milk protein additives in tons of things you wouldn't expect- some lunchmeats, many crackers, chips, canned goods, almost any boxed foods (like noodle mixes and hamburger helper type things). Anything like whey, lactose, lactulose and others I am sure I can't think of now. Your doctor should have a list of things to avoid. I only mention this because I thought I was eliminating all milk allergens (and I am an RN) and when my son's nurse practitioner gave us a list there were tons of things I was missing.
Here is a good source of information: http://foodallergies.about.com/od/diagnosingfoodallergies...
Remember that a RAST (blood) test is considered most sensitive (best able to pinpoint an allergy) but a skin test is most specific (meaning it will show if there is a sensitivity). So although a RAST test could show an allergy to milk through antibodies in the blood, the skin test will show if the reaction is actually being caused by that allergen or something else. I.E. my son's RAST test is positive for milk, soy, and egg allergy, but on the skin test is nonreactive. So we know my son has a mild allergy to those things but they are not the cause of his symptoms. So confusing. Good luck sorting this out and definitely keep up the breastfeeding.
Remember that human milk protein is different than cow's milk protein and if you can resolve this issue he will be much better off on breastmilk than on soy formula which has other drawbacks. The specialized allergy formulas are very expensive not to mention stinky (my son had to have this) and I would recommend avoiding them if possible! Good luck.