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I am not an expert but suffer from IBS myself . IBS can start after an infection . Try to take care of the hernia asap and give your son transfer factor advanced plus capsules . It is supposed to educate the immune system and correct any abnormality . I hope somebody gives you some answer . School is very important , my prayers will be with him ...
There is a term called post infectious IBS or IBS that developed after an illness. Also if the doctor suspected virus he should not have given him antibiotics. Antibiotics are only effective aginst microorfganisms(bacteria,Fungi,Protazoa, etc) they are not effective against viruses. It may have made the situation worse. Antibiotics can distrupt the delicate balance of microbes in the gut. There are cases of people who take antibiotics for other non gut related issues developing IBS.
If you take antibiotics I recomend taking a good full spectrum probiotic. Even GI docs are now considering the probiotic option (running out of options).
Check this article:
http://archives.cnn.com/2000/HEALTH/12/13/bc.health.irritablebowel.reut/index.html
If after trying to fix the hernia the situation doesn't improve you can try the pill cam or capsule endoscopy. Also in the meantime you should do the food log and elimination diet. You could try the usual suspects like gluten and lactose.