Same thing happened again today. Everything worked fine yesterday, but when I today sent 2 books and some news I downloaded with calibre I can't see any of my books any more. If I sort by 'Recent' or 'Title' I can't see any items. If I sort by 'Author' I can see all the news and the collections, but no books. I can see the books inside the collections and I can open them, but they are nowhere on the main screen.
I created some collection with calibre that I imported with CM yesterday and it worked fine. Today I didn't create or update any collections when I sent the new books. I only downloaded some news which I also sent. Maybe there is a bug there. I don't know, but I think I'm going to stick to stock firmware for now. Too much hassle just for some collections (something which should be standard from Amazon really).
When I reset the Kindle is the JB etc. still installed on it?