Well... you would expect '100% synthy' to mean that everything is connected, but sometimes the website awards a high synthy score, even though some of the images are only barely connected. The Photosynth team calls these 'portal' images as they act like a gateway from one large cluster to another but are a very weak connection. This means that sometimes when you look at a synth in 2D view, some of the images in the largest/only cluster may not actually belong to the same point cloud. In that case, only the images which are attached to the largest point cloud are available for alignment.
If you still have the log files for your synths ( %temp%\photosynther ), you can open them up and scroll down until you see 'Synth 0'. That will be the images on your largest point cloud. On a truly 100% synthy synth, that should be all that there is. If you see 'Synth 1', 'Synth 2', etc. then that is indication that there is more than one point cloud in the synth.