I also don't use the Sony software - Calibre is wonderful for organising and copying books onto the reader.
I had a similar problem with mine: I had tried to add a bunch of free ebooks, after which the software would not transfer any more files to the reader. Eventually I worked out that it was just one of books that was causing the problem and after I removed it from the reader via the filesystem I could send books to device again without any problems.
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