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This is a poser! According to one of my favorite sources, Cecil Adams of The Straight Dope, the reason for the differential is that walking is a more energy-efficient gait than running. He agrees with you that speed makes no difference to energy use, but "apparently you lose energy absorbing the impact of the ground with your bent knees" when running. You can read his full explanation here: http://www.straightdope.com/columns/read/2580/exercise-does-running-burn-more-calories-than-walking
Hope this answers your question!