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Try using the current gmapping version from github. We just build a patch some days ago to make gmapping work under such conditions. I dont think, that this version is already getting distributed through binary updates.

How did you tell the robot, that the laser is upside down? By setting an apropriate transform? Is the visualization of the laser scan in rviz correct? If so, the new version should work. Otherwise it will be helpful, if you could post a bag file containing odom, tf and the laserscans.