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octomap_server uses PCL with pcl::SACMODEL_PERPENDICULAR_PLANE to detect and segment the ground plane, which has quite a few parameters to tune. Right now it should work best with stereo data from the PR2, laser data from the Velodyne might need different parameters.
Best have a look at OctomapServer::filterGroundPlane and the PCL documentation on which parameters to tune, ground_filter/distance and ground_filter/angle should be the first ones to try. You can also do a rough filterung just based on height with ground_filter/plane_distance.
Otherwise run rxconsole with setting octomap_server's log level to debug to see what is going on.
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