Lemme try to explain better, because it would be awesome not to have it happen again...
Sometimes when adding new books, recreating collections, etc, Calibre will "forget" that the books on my Kindle are in its library. When this happens and I look at device view, the titles of the books reflect the titles as they appear after applying my plugboard (with series info in front of the title). When this happens, they no longer appear in collections (as they are no longer known to be in Calibre's library). The not ideal solution is to remove the books from the device and the add them back again, so Calibre knows which book is which and can put them back in their proper collections.