I've had so many problems with the Sony Reader that I've just uninstalled it. It's confusing and frustrating buggy crap, and I'm sure rushed in development. It'll probably take a few generations for them to sort this out.
The good news is that you don't need it at all. You can move files to it through the windows explorer. And as for the fancy functions Calibre does it better than the Sony Library anyway. So... just delete and ignore.
I've managed to buy books to it in other shops in other formats and converted them. That's a nice thing about the Sony Reader.