As far as I can tell, the screen saver patch did indeed block the update to 2.0.1. I removed the patch and the update went through just fine. I had to restart a couple times before I could get the screen saver patch reapplied to the new version.
Current version string is: Kindle 2.0.1 (303870012) + Screen Saver Hack 0.3
Hopefully this helps someone.