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I had a similar issue, but not quite the same as you. I will not offer you a solution, but rather some links that may shed some light on your problems...

https://github.com/ros-planning/navigation/issues/267

http://answers.ros.org/question/32633/costmap-2d-kinectlaser-clearing-problem-when-encountering-objects-with-thin-legs-eg-tables-or-chairs/

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