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Is your kinect mounted upside down? You say that you see that the scan is in the correct orientation, so I assume that this is in RVIZ and relative to base_link?
If that's the case, what are min_angle and max_angle set to? Is should be that min_angle is something like -pi/2 and max_angle is pi/2? And then the angle_increment is positive?
If all of those are the case, what version of gmapping are you using? The newest ones use the TF data to reverse upside down scans. You may want to try running with inverted_laser being set to true, but this was been removed/deprecated as of 1.1.1. You can see more at the gmapping docs.
These are good first debugging steps. Let everyone know what the results from these are.
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