I must be the only lucky one that hasn't had problems with Windows 7 64 bit and the Sony software. Have you emailed Sony support? Have you tried uninstalling then reinstalling the Sony software? You can save all your books to a CD or USB before doing so, then you can add them back later.
I did the same syncing thing as you once. I just deleted the duplicate books one by one from the reader and made sure never to click that sync option again.