Welcome to the gastroenterology community! It might be celiac disease. He can have a blood test to test for this and it can be treated by removing gluten from the diet. My personal belief, although everyone is entitled to their own opinions, is that as long as you are microwaving in microwave safe container, microwaving is perfectly safe and from the research I have done on the internet, I saw no properly conducted experiments by large companies proving otherwise.
The digestive tract is very important. Children can take probiotics. More FRESH FRUITS AND VEGETABLES. The body cannot properly digest Microwaving foods so cut that out of his diet also. (Check web for dangers of microwaving). Hope this helps.