I went through a period of having dodgy guts, and having recently read an article about modern bread manufacture methods, and how they basically suck, I tried a week without bread, believe it or not (not easy to do actually) and I'm feeling a lot better for it and have been off bread ever since. Hard to believe but this faux diagnosis I applied has seemed to have worked.
Of course, I'm no health expert, but it may be worth trying to eliminate certain things from your diet. I have a friend who's a nutritionist, and he says that mild intolerances to, e.g. gluten, are quite common.