I've had GI issues since my mid-twenties (over 20 years), finally got rid of them a couple of years ago in large part by eliminating gluten. Aside, how I discovered that was I went on a VLC diet with a "cheat day" on the weekend, usually w/ pizza as the main meal, and invariably by mid-week of the following week I'd have the symptoms return for a day or so. I finally tied that back to the pizza (yep, several days would elapse; made it alot tougher to pick up the pattern), and from there specifically the gluten in the pizza through the process of elimination. I'm not VLC anymore but still gluten restricted. That took care of about 80% of the problem; most of the rest was helped by soluble fiber / prebiotics, usually in the form of Inulin FOS, but arabinogalactan worked well also if FOS causes you problems on it's own. Note that there may be an adjustment period once you start using a soluble fiber.
Since I started SS and supplementing whey protein w/ milk, I've stopped the dedicated soluble fiber supps as whey (and/or milk) can act as somewhat of a prebiotic also, apparently (and that's been my experience as well):
http://www.ncbi.nlm.nih.gov/pubmed/2312674. No problems keeping things moving normally (at the least) w/ either soluble fiber supps. or whey/milk. Oh and a decent broad spectrum digestive enzyme helped out early on also, but I don't need those anymore either.
If you're skeptical about grains/gluten being a problem (and maybe in the end rightly so in your particular case), consider picking up the book "Wheat Belly" by William Davis. It does seem full of hyperbole but it's an easy read and there is some good stuff in there, or at least fodder for additional research.
Good luck, hope this gives you some ideas.