After clicking 'omitted', the box with images that were omitted does not always show all omitted images.
There was some discussion of this in this older discussion:
Look for the Photosynth team's first reply and then my reply to them, specifically where I say "the listed number doesn't seem to correspond to the number of thumbnails displayed. Could you help me understand better?" and David's follow up.
Thanks Nate. Just ran into the new release. Learning time ;-)