I guess I just don't quite understand what you have going on. I just know that MBPs are not ebooks. They're ebook
companion files. I don't add them to calibre. Ever. Maybe some people do -- since they show up under the Files of type "Book" filter of calibre's "Add" dialog, after all -- but I don't.
If you're adding books to calibre from your Kindle for PC library (the "My Kindle Content" folder). You're
always going to see MBP files there. You can delete them from that folder all you want, but whenever you open a book in Kindle for PC (or download a new book), they're just going to be created all over again. You're fighting a losing battle. There's
supposed to be MBP files there. You can't stop them from being created there. You shouldn't try.
I'm not exactly sure why you're only now having this issue, but I can assure you, it's not because of Alf's newest tools. Something has changed in your normal workflow, is all I can figure out. Have you
always been adding books to calibre directly from the My Kindle Content (Kindle for PC) folder? If so, you should have been seeing the MBP files all along. Because they've definitely been there all along.
Changing the "Files of Type" filter on calibre's "Add" dialog won't get
rid of the MBP files, it will just filter them out so you don't
see them (temporarily). But you really should ultimately find a way to live in peace and harmony with MBP files, because frankly, they ain't going anywhere. Just nudge 'em out of the way (sort by Type) and keep going.