A couple things I've heard (the first from my naturopathic doctor)
A food allergy may not cause an extreme reaction (like, say, anaphylactic (sp?) shock or hives or itching, etc). Instead, it can come in the form of GI upset and repetitively introducing the allergen can increase the reaction...maybe reflux?? (For example, I didn't want to believe that chocolate could really cause GERD and yet every time I ate it, I would have this horrible feeling in my mouth and throat...I had allergy testing done and was highly allergic to chocolate (bummer for me

) ...so maybe it didn't cause GERD in the way it's typically thought to, but rather in the form of allergic reaction.
Also, I'm reading a book on stomach acid and read that the PPIs stop acid to the point that food may not get digested and broken down and then the proteins "may" get into the bloodstream where the body senses it as an invader so food allergies could develop...
I don't know much more about this as I'm still learning myself.