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The issue you are facing is probably related to how the plugin re-partitions the duplicates based on exemptions list. I don't have the time right now to dig deeper into it. Maybe will return to this in the future.
My guess is that if you remove all the exemptions (after backing them up), the problem will disappear. You can backup the settings this way: Find Duplicates > Customize Plugin > View library preferences > copy the preferences to a text file.
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