Originally Posted by Tome Keeper
Not sure if this is a plugin, Calibre or Kindle issue really.
I'm using the Kindle Collections plugin to organise my books and it all worked well except about 30 of my books have not gone into collections on my Kindle when they should have, and I have done the same thing to them as the others. I have also restarted the Kindle (from menu) several times but no luck.
Try deleting the books from your Kindle, then restarting. Now add the files back and then write out the collections settings using Create from the Collections menu. (And restart again, of course.) I've seen this happen a few times with books that somehow have a slight disagreement between the Kindle and Calibre about which book is which. The Collections logic seems very sensitive.