Dan,
Glad to see my suggestion worked for you. Over the last week I have been similarly trying to remove more corrupt data from my library of over 25,000 photos. The corruption I see is as described earlier, plus the small square boxes you describe, plus more:
tiny boxes with essentially no area at the lower left corner of the photo
photos with no found face box yet the Info pane lists names of found faces
large square boxes labled with a correct name but in the wrong locations in the photo
found face boxes appear correct but the thumb is from some other part of the photo
found face boxes appear correct but the thumb is rotated 90 degrees
Probably there are others that I do not remember right now.
As might be expected with this level of incorrectly identified faces, prediction of matching faces has been poor. As I have deleted obvious corruption from the database I have also verified correct predictions and marked incorrect predictions. Predictions are now much better.
This corruption remained after merging three libraries using iPhoto Library Manager, then doing all of iPhotos internal rebuilds several times, then rebuilding the library using iPhoto LIbrary Manager. When I finish removing what corruption I can manually I plan to rebuild everythng once again. Even with all this cleaning I am concerned that I will miss some corrupt data, and the corruption will propagate.
I have not heard of using MySQL on Faces or iPhoto. Directly manipulating internal iPhoito structures sounds like asking for trouble, but we already have lots of trouble with no apparent solution. I will investigate. Thanks for the tip. Have you tried it?
Tom