Jim, you may actually be witnessing an imperfectly joined pointcloud. For what I mean, read David Gedye's reply to this synth: http://photosynth.net/view.aspx?cid=FB5BF8DB-1FFC-4D75-81C9-3711BD29A032
If that is the case, as with synths that are less than 100% synthy, only the highlight indicators that reside within the primary pointcloud will be displayed in overhead view.
As for the highlight indicators being 'out of alignment' with overhead view, I can't say that I'm reproducing that error, so I don't know for sure whether I understand what you're saying, but I assume that you are aware that whenever you are on a photo that is connected to the primary point cloud that you enter overhead view on the vector or orientation of the last touched photo.
The main reason that I suspect that the 'up' highlights are not connected to the main pointcloud (even though you have 100% synthy) is that there is no animation to overhead view, but just a jolt.