Photosynth can only create point clouds for parts of the scene seen in multiple shots and that would explain why you're seeing bands of points (where your columns of photos overlap).
Photosynth can only estimate depth for a portion of the scene that is seen from multiple perspectives, however. It is not sufficient when creating a photosynth, rather than a panorama, to shoot from a single perspective.
Since you have a great panoramic head to work with, I'd try taking a minimum of two panoramas several feet from each other to give Photosynth some parallax to work with and put both sets of photos in a single synth. That should result in a much more constant point cloud and given the multiple perspectives, should take you away from the flat sphere of points that panoramic shooting yields.
For more on how to get the most from Photosynth, please read the Photosynth Photography Guide available from: http://photosynth.net/help.aspx#photosynthhelp