Dave, coffee quite often upsets my stomach as well but possibly not to the same extent. Do you notice any difference if your stomach is empty or if you have a coffee with food?
If I drink it after a meal, like fifteen or twenty minutes, no probs. With a meal, like breakfast or late in the arvo (about three or four hours after lunch) by itself, its potty time.
But in both cases you could say its on an empty stomach, so you might be onto something.