I am not quite sure of what you're saying because you describe a right hand panel. Also, if you read the description of how the de-duplicator works, all of those things showing up in the only panel that it has when you do the search are duplicates. From the add-on page:
To remove duplicate bookmarks, navigate to the Add-ons Manager, open the Bookmark Deduplicator preferences page, and press Search.
A popup showing all duplicate bookmarks will be opened. After a confirmation your duplicate bookmarks will be removed and the amount of removed duplicates will be presented.
This part of the description is inaccurate. What the popup is showing is actually a list of all your bookmarks. I do not know why they say it shows only duplicates, because it does not.
After you confirm, it will tell you how many were actually duplicates that were removed. I just did my own bookmarks after having made a backup by exporting them to HTML in case something went wrong. It told me that 67 duplicates were removed, which seems about right, and my bookmarks still appear to be just fine.
Note: Bookmark Deduplicator will sequently [sic, should be sequentially] read the addresses of every bookmark and mark each one that points to the same address as a previously checked one for deletion. Consequently, the bookmarks that have been checked first - usually higher up in the folder hierarchy - will not be affected.
This is the actual behavior I've seen. It starts with bookmark one, scans bookmarks two through end and deletes any that are the same as bookmark one. Then it moves on to bookmark two, scans bookmarks three through end deleting any that match bookmark two. Etc., Etc., Etc. Thus, the first occurrence of any duplicated bookmark is what will be preserved while all duplicates that are further down in your hierarchy somewhere will be deleted.
They just incorrectly described what shows up in that box when you hit the "Search" button as being *only* duplicates. It isn't, it's all your bookmarks that will then be processed to remove duplicates when you hit the "Remove" button.
When I try the "Search" after having done a "Search" and "Remove" cycle no duplicates are found and no pop up window with the bookmarks appears.
After you've made an HTML backup for safety of all your bookmarks try this and you'll see that it works.