From what it sounds like, Noah might've had the same issue with his Ark in conditions like you describe. I recently swapped crank sets between two bikes, then two nights ago (about two weeks after the swap) disassembled and cleaned the BB. There was stuff in there, not much, but despite a nice coat of grease on the shell and teflon tape on the cup threads, junk got in there. With the amount of rain you saw, I would think you are maxed out with sealing off the frame from water. Sometimes it just happens.