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That must be because you are using Shelves. I am using version 1.5, but have never used Shelves and my arrangement still looks like it used to look under 1.4 - i.e. when I go into My Library, the top entry (on the bottom panel) is either "Go to My Documents" or "Go to My B&N Library", and I am only seeing on the main panel what is in My Documents or My B&N Library (the opposite of what the bottom panel allows you to "go to."
When I first got my Nook (1.4), I had exactly the same problem the OP is having - I'd sideload books using Calibre but then sometimes couldn't find them, when I had used My B&N Library the last time I'd used the Nook. I'd go into my library and only see the B&N books, and couldn't see any way to get to My Documents because that "go to" optioon was not appearing on the bottom panel because it had scrolled off of it. I didn't notice the scroll bar on the bottom panel. I'd be sitting there wondering how to get to My Documents.
I don't know if this is the problem the OP is having, but it sounds like what happened to me.
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