M.B.
First off, I'm not a doctor so this is just advice (I see so many people on here offering advice as if they are experts, I am not as are not most people responding and anything you learn here should be discussed with your doctor.)
So this is just a suggestion to look into if it continues.
Is he eating bread, cookies or anything that contains flour or grains before it happens?
My experience is with a friend whose son started to have severe bouts of diarhea. Some days he didn't have it at all, other times it continued for weeks. They kept going back and forth to the doctor and they would never find anything wrong. It got so bad and went on for so long with no answers.
Finally, he was diagnosed with Celiac disease. Once they eliminated gluten containing foods from his diet, he was fine but they have to be diligent.
This is a write up on Celiac here
http://www.kidshealth.org/teen/diseases_conditions/digest...
That is a worse case scenario possibility. Another thing could just be a food allergy. Food allergies of any kind can cause GI upset.
Start keeping a log of EVERYTHING he consumes in a day. (even drinks) and start comparing what he's had with when it happens. Slowly eliminate one of those things that he has daily for a few days and see if it stops or slows down his diarrhea.
There's a nice write up here on food allergies
http://www.askdrsears.com/html/4/T041800.asp#T041803