yes.. that can be a problem wit hdigestive.. since he is totally clean... he brushes his teeth which most of the times causes bad breath or halitosis. i suggetst he avoid eating spicy food since it creates the worst smell the most...
try listerine (sorry for bad spelling)
or any other type of mouth wash.
also keep note of what he is eating, because some foods just have that bad breath affect.
Definitely see a doctor. There could be an obstruction in the digestive tract, or something very simple. It should not be ignored though. Has he seen a dentist to rule out any oral abcesses?