The pain is short living The pain is short living after the run, therefore generally it does sound (from my limited knowledge) more like neuroma. For a stress fracture I understand that the pain would not simply go away after short period of not moving the parts in question. I've had at least two (upper tibia left leg, left foot - felt like what I would now call TMTS) in my short running life. Last xray (2 yrs ago) I had for that one showed that the foot one healed without treatment, haven't had the tmts hurting since then. This pain is only short lived after the run, it goes away quickly. However it's status did not change over 12 month. Not better, not worse. It never happens with even pretty flat shoes (like asics hyperspeed 4). It happens with VFF however and barefoot even earlier.