Check the Kindle's sorting order.
In the main library list, make sure you are sorting by collections. That will pin collections to the front, and also make the books in collections not show up outside collections... because if you sort by Author/Title/Recent, then collections appear alongside
all books.
Inside collections, make sure you are sorting by author. It should fallback to title (with inserted plugboard-based series) when multiple books have the same author.
(Really, this is a Kindle issue, not a calibre one. See our
Kindle forums.)