Question
I'm having pain on the outer side of the foot closer to where the bump of the ankle is on both the right and the left.  I'm fine when walking but when starting to run, it hurts for the first 1/2 mile goes away and then comes back.  Also I've been having pain on the back of the heel more where the achilles tendon joins, but it only hurts when i point my toes.  
I've had plantar facitius before and had surgery but that was a year ago.  
I've been running with vibram five finger shoes and it has been working even though I was sore initially on the top of the foot and front of the leg.

Answer
If you're running in the Vibrams, it's imperative that you are running with a forefoot strike (not heel strike), shortened stride, and bent knee.  I've seen many injuries for those running in Vibrams, so you should consult a coach knowledgeable in the proper technique.  If the pain persists, stop using the Vibrams and consult a podiatrist for evaluation of your mechanics.

All the best,
Andrew Schneider, DPM

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