I'm not about to play WebMD on here and perhaps kiddiedoc can really help here, but the fact that the pain goes away as you stretch it and run on it, is a natural symptom of a very dirty two word foot problem.
You going to start training for a tri?
It is a very long range goal. I have certain PR times in a half and full marathon this fall I want to hit before I really get into going to do a tri, but I'd definitely need to improve my form for swimming and it's just a great all around workout.
I also need to buy a decent enough bike to carry me through a tri.