I have experienced that sensation--I have IBS-C.
Question--when running, do you wear anything that may be tight around the waist, like spandex? Anything that's even remotely tight makes my IBS flare up. I noticed the spandex thing myself, and since I started wearing looser clothing, I never have any trouble when exercising. In fact, exercise relieves my IBS symptoms (cramping, bloating) when it's acting up.