I also have the same problem as Tylermckellar, I synched last night and the books that show when the home button is pressed jumped from the 11 I had on there already to 44 (including the 7 the synch put on there).
All of the books that I had not bought, but were put on my kobo wireless locked on the loading screen that displays the front cover of the book and I had to switch off and switch back on. Also it put another copy of at least 10 of the books I had already purchased on the ereader.
It took me 1 hour and half the battery (which was full) to remove the unwanted and unreadable book from the ereader.
This is not the first time it has happened, in fact it has happened every time I have synched it since the latest version of the desktop application was released.
As you can tell I am not happy as before this problem it was a good device. I would love to know how to prevent this from happening again (without reverting to an earlier desktop).