Trust the Results?

I'm so stinkin confused...but to explain what I'm confused about, let's start at the beginning. So when Caden was born he cried. A lot. Now a lot of newborns cry a lot, but his was often the "something is bothering me" cry. He also had a skill. A great skill. The kid could projectile vomit within a 5-6 ft radius without any effort. So, we determined he had reflux and got him the meds for that and they worked like a charm. We also determined he was sensitive to milk.   I assumed it was a lactose issue, common for little munchkins such as himself, and tried soy formula (by this time I was having to supplement nursing with formula because everything I ate upset the dang kid and he threw up everything I fed him anyway, so I never had enough). He broke out in a horrid rash all over his face and torso and had, let us say, diapers that labeled him allergic to soy. So we went through the whole Alimentum/Nutramigen journey and frankly that stuff it just putrid. I couldn't handle the smell and Caden started just flat out refusing to eat. Long last we settled on Target's brand of Similac Sensitive and everyone was happy.
Fast forward to him eating solids. Everything was great, no issues - until we got to graham crackers. Same diaper issues return - blisters, tubes and tubes of Desitin and a very unhappy baby. Then the same thing with Ritz. And Cheese-its. And some commercially make breads. And granola bars. And McDonald's french fries. And the list of processed foods goes on and on. Common ingredient between all of these? Soy. At least some form of it. So finally after a long two week stint of reactions to something I couldn't quite pin down, I asked his doctor if we could get him tested to figure out how severe this allergy really was and what the chances were of him growing out of it. So, after getting two shots, we drug the little man down to the lab and had four adults hold him down while they took a vile of blood from his arm. (So sad - and yet still better than changing those owie diapers...) Then Caden enjoyed his first sucker. He held on to that thing like a lifeline and licked it to the stick - he wasn't terribly messy either!
A couple days later the nurse calls me with the lab results. Verdict? No soy allergy. At all. However he is apparently highly allergic to cows milk. And mildly allergic to peanuts. WHAT??! So I do some research and discover that all the things he's reacted to do indeed have some form of milk protein in them (minus the french fries...and he eats peanut butter and jelly sandwiches frequently without issue). Okay, that could make sense. Except for one little detail. He has NO problem with milk, yogurt, cheese, butter, ice cream, etc... In fact, milk, yogurt, and cheese are a HUGE part of his diet - sometimes all he'll eat. So I guess we're no closer to figuring out what the heck this kid's issue is than we were before. If anyone has any experience with a milk allergy - especially if it involved them being allergic to milk proteins in any form BESIDES dairy (pretty sure that's not possible...), I'd love to get your perspective. Otherwise, I'm deeming these blood results incorrect - they just don't make sense - and we'll just stay away from the triggers with no idea why they're triggers.