At first I just dismissed this as a generic bug without looking into what was specifically going on.
When I click on all categories for example and then have it scan for dupes the page refreshes with zero dupes found but I notice that only the first and second level cats are checked off in the list. Infact it won't even check off the 2nd level cat that has a category underneath it.
So for example I have a category structure like this:
In this case City will remain checked, but restaurants or Restaurants1 will uncheck themselves.
I have other 2nd level cats like news and jobs and those remain checked as they are not the parents of further categories. Because of this the plugin can not find the 1000's of dupes that lie within the 3rd level of categories