It's a problem with Ubuntu... I had the same problems... I just uninstalled it and then got the most current release using the instructions on the calibre site, and my PRS-300 works perfectly now. Kovid puts out a new release almost every week, so it's better this way anyhow - easy to upgrade and have the most current features.
I usually hate going outside of my apt sources, but calibre is moving so rapidly that I don't mind in this case.