I have two folder trees displayed, and when I tell DOPUS to ignore the word "The " for instance, the first tree does not display properly, but the second one does.
I don't know how you filtered the folder names.
You wrote Ignore prefix when sorting which as far as I know is in preferences at Preferences / Filtering and Sorting / Sorting .
But that only puts the ignored prefixes at the top of the lister sort as I understand it.
It seems from your screenshot that you have filtered out any filenames beginning with the word The .
I clearly see the problem though !
One tree filters and the other doesn't !
Your post caught my interest in part because of the Alicia Keys folder.
One of her videos was filmed in a small hotel in New Orleans ( The Columns ) that at the time was owned by the family of a more than old acquaintance of mine.
The Fire We Make
If you only type in "The", without a space, all of them will indeed show up at the top of the list. Someone posted a few years ago about the issue, and the solution was to write "The " with a space, when ignoring prefixes.
That's a nice Alicia Keys video, and hotel, BTW.
Folder Format options affect the file display. They don’t do anything to the folder tree.
This should hopefully be improved in 13.16.9.
Great, thanks.
My folder tree looks much better. It was disconcerting to see the folder tree not in the same order as in the file display. Thanks. 
Edit: I took a look in the preferences to see how you did it. Very nice.
