CC doesn't keep any last read positions or any other information from inside the book (bookmarks, annotations, etc). Those are solely in the hands of the reader apps. When you "read" a book via CC, it launches the reader app and gives it the name (path) of the file in CC's library. What happens then is up to the app.
I use moon+ pro. For me, when I launch moon+ from CC I get the last page read. The same thing happens when I read the book using one of CC's desktop widgets; and when I manually launch moon+, select the book in the "Recent list" and then read it (although I never actually do that). I don't use the moon+ "library" and I don't know how using that feature will affect the reading position stored by moon+.
My guess is that you have two copies of the same book, one in the moon+ "library" and one in CC's storage. Opening one will get you the reading position last used for that copy. Opening the other will do the same, but for the other copy.
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