In reply to cap'nChino:
Sounds very much like acid reflux.
I have it very occasionally but almost always with an obvious cause. Running too soon after a big meal which is hard to digest. White meats etc go down easier, even maybe knock out dairy as we can be intolerant without really knowing it.
See a Dr but in the mean time play around with your diet, how long you wait before a run, maybe even eat more frequently but less when you do. Drop out the obvious food groups, dairy, red meats at lunch etc.