Okay, I think I solved this one, but tell me if any of you have experienced this before: The spot on the head of my penis never developed into a pimple, it just stayed kind of red and a little puffy. It kept feeling raw when I would exercise, and therein lies the, ah, rub. It kept coming out the barn-door of my boxers and rubbing against my shorts. Before any of you lecture to me about wearing boxers while exercising, let me just say that it hasn't caused a problem for me before.
Ever since I changed to "tighty whities", things have settled down. Stupid answer to a stupid problem, but there you have it.