I got a PRS300 last year for christmas as well. It's a great reader but the PC organizer software just plain stinks. I have since switched to Calibre (it's Free! Really) You can get it here:
http://calibre-ebook.com/
By the way, you don't have to buy books from Sony either. You can get books at Kobo, Smashword, and Baen books just to name 3. (A bunch of others too)
In the meantime, What I would do when the Sony software doesn't seem to launch, try turning off the computer and then back on. And then, instead of letting it launch by plugging in the reader, try launching it by clicking the icon on your screen and then connecting the reader to the PC. When I get this problem this sometimes helps.
I'm discovering the less I have to do with Sony, the happier I am.