I wonder if you force a "Reintegrate Forgotten Catalog" maintenance operation if that would correct the problem? Give that a try.
Sadly, that didn't work.
Alternatively, you could remove everything and then do a Full Sync and it should add them all back in. If it still gets duplicates then I want to get to the bottom of that, ASAP.
Interesting, I tried this on one of the folders+subfolders with duplicates. Selected all images, executed remove from catalog and then – surprisingly – was presented with the just one version of the duplicates still there (all other items were gone though). So they are simply very stubborn
(guess I hadn't noticed this the first time I tried to remove both versions of a duplicate)
Another try: I noticed that the folders with duplicates showed up twice in the browse view (each time with the correct number of images, but viewing the folder gave the duplicates again). So I then tried removing a duplicate folder from there. One of the offending ones did indeed get removed, but the second one didn't. And when I then did a sync, the duplicates popped up again, but the folder then did not duplicate itself.
As a further attempt at solving this, I removed one of the proxy files (there were two identifiable ones) for a duplicate image and removed it again from the catalog. Sadly that didn't help either (one version did not remove and the image is still duplicated after a sync). Now there is only one proxy file left though. But now I again have the directory in the browser twice, with different counts)
I've attached an image of the browser with two problematic folders.
If you can think of anything more I can try to help you identify and solve this issue, please let me know. Otherwise I see no other solution then to rebuild the catalog from scratch.