Have you experimented with what you eat? Things I am thinking of are, for example, eating something that is easier to digest (a banana, maybe, or pretzels), not having all in one go, but a bite every 15 minutes or so... Also, could your shorts be to tight around your waist? That, plus the normal leaning on the bike, can be quite uncomfortable. RoadID sells some Giordana bib-shorts at a very reasonable price for testing...