Thanks for the file.
Look for a fix in 17.0.72 and newer. Hopefully it will be available in a few days.
Carnac can cause the Name field to be a little different from what the tag reader returns, and this caused the 'skip duplicates' feature to compare two different names (it also compares several other pieces of information, but these weren't a problem).
We switched to using 'Filename (name)' instead of 'Name', which fixes the issue. This makes more sense anyway, because it may not be that rare for people to give an image a meaningful name so using the filename should be more robust.