Collections on 4.1.1

[jeep123]

I have recently been just throwing books onto my main screen via calibre, but its getting crowded and I need to put them back into collections.

In the past I have used calibre and kindle collections plugin, clumsy with the restarts and all that but it works.

However, I assigned collections to my books and deleted them from kindle and re sent them over with the new collections. Restarted and it seems only some of the books got assigned to the collections? But most just stayed on my home screen. What gives?

How do I fix this, I love my kindle but the collections thing is driving me insane, almost enough to get a different device when I get something with the 'paperwhite' scheme. Almost, but not quite.