CC doesn't support syncing using USB. Books transferred that way don't appear in CC's database.
As for transfers using the content server: are you using the demo version of CC? It is limited to 20 books.
I am confused about what you are saying about the green check marks. Are you saying that CC's content server connection screen shows a green check mark for a book, but when you return to CC's main list that book is not there?
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