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Ar_kinect basically uses ar_toolkit to find the four corners, then uses the depth information to refine the 3d pose. If any of the corners has no depth data, the registration fails. Unfortunately, there isn't much you can do if you just don't have depth data at some angles.

I just applied a patch that has been sitting on our issue tracker for quite some time which should clean up the NANs. (which is a more graceful way to deal with missing points than publishing horribly NAN transforms). If you pull the trunk again from SVN and rebuild you should at least see the NAN issues go away.