Try having your son take digestive enzymes with his food, proteases with protein, lypase with fats, amylase with carbs. etc. This can solve a lot of problems. A good digestive enzyme complex will have all of these.
Slippery elm can soothe the stomach and intestinal tract and is very healing.
My other thought was he might have a physical injury. Consider getting a body scan done if it continues, or if he begins to have more pain or other symptoms.
Enzy
could be vitamin defficiency, could be H.pylori, Could be chronic gastroenteritis, could be appendicitis...doubtfull though, could be diabetes, could be lymphonodular hyperplasia...but doubtfull, id go with other infections that the doc might now have ruled out look on web md on the symptom checker see what it says...but look up H. pylori...good possibilty...along with vitamin deffiency