Triffnix Thank you very much for providing samples of problematic files!
They indeed contained some strange combinations of data and we were able to fix couple of bugs cocerning edge cases of data synchronization. The issue is connected withe fact that there are multiple instances of same face with slightly different coordinates in your ini files, and they might be also different from locations where program finds those faces on the photo.
Program tries to do fussy compason allowing some wiggle room for coordinates, but there could be thousands of cases where this might go wrong. So, few of those cases we were able to identify thanks to your samples. We added some additional checks there, and we believe that there should be no more situations when new duplicate faces appear out of nowhere.
However this does not resolve the issue that your ini files still contain some strange data, which was the cause of the problem in the first place. Hard to say what was the initial reason of this coordinates discrepancy, probably those accumulated over time as Tonfotos recognition module evolved.
Those fixes will be part of the next release in few days. After update, if you would re-index those problematic files, few of the issues will just go away (at least it will look like that), but for some files not, as problem is already stored in the ini files. So, you probably will need to do some manual cleaning nevertheless.
Also, after that cleaning is done, I would recommend to delete all tonfotos.ini files from your arcive and let program to recreate those from the scratch. That will make old corrupt coordinates to go away completely, only actual coordinates will be stored again.
Sorry for all that trouble.