Hmm.. you might want to post your error in the Calibre section and let Kovid help you with that
In any case, I read so many horror stories about the Sony software that I never even tried it - didn't even install it on the Reader, just started out with Calibre. Of course, I've also spent the last month adding all my books to Calibre and fixing metadata and getting them all nice and neat (and I didn't even know I was buying a Calibre-compatible reading device!).
But maybe the software could be a contributing factor to your problem?