Can't speak for any children except myself--
As a baby I would spit up a lot. As a young child, this turned into throwing up more than was probably normal (I couldn't burp without throwing up until I was 6).
In elementary school I often had a stomachache after eating lunch. I didn't eat breakfast before school because I never felt well when I ate breakfast either.
Starting around middle school, I would get diarrhea after eating almost anything. In high school it got worse. In college I was diagnosed with ulcerative colitis.
I was 26 when I found out I couldn't have gluten. There were a million signs before that, but it was never on anyone's radar. (Except a friend who suggested it back when I was about 20 and suffering from some weird nutritional deficiencies that we blamed on the colitis.) And don't even get me started on how my parents just ignored all my pains. My mom worked in my school, and every day I would tell her I felt sick after lunch. And every day she blamed it on recess, even when we had indoor recess. Which doesn't even make sense.
So my advice is ... don't be like my parents. Monitor it, keep track of what he's eating, and keep track of what kinds of symptoms he's having after he eats that. It could be another food issue. It could be something worse like colitis or crohn's that hasn't really, uh ... blossomed yet. And I say that not to scare you, but just based on my own experience. So I'm glad that you're taking his complaints seriously, and I hope you figure out what's going on.
(By the way, I also have a family history of colitis and colon cancer on both sides, and I know what it's like when people don't think that's relevant. Frustrating!)
You're story sounds like mine, expect my mother took me to specialist for years and they all thought she was "over involved". But yeah, symptoms as a child, always feeling ill, always vomiting, chronic nose bleeds, ulcers etc. I was only after she as diagnosed at 65 that we started looking at me. Hindsight is amazing isn't it?