There is a simple work-around to this issue. When you download a book from the Sony store it is save the file in your 'Documents/My Books' folder'. You can manually copy the file to your Reader by dragging it to the 'Untitled 1/database/media/books' folder on your reader's internal storage.
There was another, much longer thread on this issue several weeks back that explains exactly what is going when OS X is booted to the 64 bit kernel.
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