@kjancaitis: almost all of the "problems" that you are describing seem to be related to you having
moved the book, instead of copying it.
In fact, everything but the last symptom you described ("Fiction collection says it has 1 item, but when I open the collection it says 'There are no items in this collection.'") is totally expected behavior, and is exactly how CM is meant to behave.
That last symptom may, or may not, be related to FW 5.4.2 -- I can't tell from your post, because you didn't mention your firmware version.