Calibre was recently changed (around two weeks ago IIRC) to scan the entire SD card for books, where it used to scan only the Sony subfolder. Is it possible that you have other 'ebook stuff' on the card that calibre is finding and adding to the Sony database? It could be that the 600's firmware cannot handle that.
You can turn off the global scan by going to preferences -> plugins -> Sony and unchecking the "Search for books in all folders" box.
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