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I had the same problem with my new NC running 1.0.1 just now.
Transferred O'Reilly ePub files to the main memory on the device with Calibre.
They show up under My Files > Books > authorname > bookname.epub
They do not show up anywhere else.
Deleted all of them via USB connection, powered off, powered on.
Re-sent the files. Ejected. Everything was there.
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