When i was a child i used to get butterflies in my belly whenever i was nervous or anxious they would sometimes feel like knots in my belly if i was really worked up. I would say something is going on at school to set off those "belly pains". Maybe the teacher is misinterpreting him being popular as him being bullied by a large amount of children.

Maybe you could try getting him to speak with a counsellor or setting up a meeting with his teacher. If all the tests show hes perfectly healthy i'd say its psychological.