I really don't think it has anything to do with Calibre. I think you might have to have the Sony software installed on your computer for your reader to charge properly though. When you plug it in, as long as the red light on the reader (I'm assuming that the 300's have the same red light the 505's do) is on, the reader is charging.
I do know that I had my reader plugged in to my computer, but used the button to eject it within the reader software. At that point, the battery stopped charging and actually started draining.
By the way you can have the Sony Reader software and Calibre installed on the same computer, just don't run them at the same time with your reader connected.
dordale