Welcome to MobileRead, pillbox. Did you solve your problem?
Sounds like it might be something with your sync settings. Here are some instructions from the Kobo website.
http://www.kobo.com/help/en-US/artic...?products=Sony
Do you really need the sync capabilities? I would just manually transfer the books on to the reader via the USB cable. Your reader should show up in your Explorer window as an external drive/device.