well, i have always heard and been told by our own paed GI that the tests for LOs are not very accurate. 50% is the stat he gave me as well. i do think that the blood test can be more accurate than the skin prick. tbh, i wouldn't be sure who to listen to either!
alimentum DOES have milk proteins in it, it's just that they are hydrolyzed, which means broken down into very small digestable bits. for MOST milk intolerant/allergic babies they are broken down enough, but many LOs need them broken down completely - and hence go onto a fully elemental milk (such as neocate).
the other thing is, just because your LO isn't allergic doesn't mean he may not be intolerant. fine line of difference, really. allergy is an immune system reaction, intolerance is a digestive system reaction. so if his bowel cant digest the milk proteins it does not mean that he can have it, and that he would test positive on an allergy test. i don't know much about the scope that your GI did, but i suspect he was looking at the bowel for damage that would show intolerance? not sure.
don't know much about blood in the stool and why it would clear up for a while and then start again. don't know if i have answered your questions or helped at all, but just wanted to share what i know until someone else comes along!
hope that is of some help. and hugs in the meantime while you sort out what's going on. i hope LO is okay!