I should mention that transfering non-DRMed books, even large PDFs that I have created, work fine. My main problem is with the Purchased folder. I did notice this evening that it works a little better when I sign in to the Sony Store, but I still get a lot of application crashes. And when it does work, it is very slow.
I also notice that most of the time eBook Library opens when I plug in a Reader, but occasionally when I plug my 300 or 600 into the USB I get a Vista message stating the device (my reader) needs to be formatted and asking if I want it to do so. So there does seem to be a driver issue as well.