I just want to share my experience because when I tried to look this up in the Internet I came up empty and I know my Google-fu is rated pretty good. I apologize in advance if posting this seems presumptuous.
Factors that might be relevant:
1. My Kindle which hasn't been updated since 3.1.
2. Duokan Install from Flip's which has not been updated since 2010/early 2011.
3. My Lenovo netbook which runs Windows 7 Starter Edition.
It all started when I unplugged my Kindle after
my netbook has deemed it safe to unplug. My Kindle's Duokan is the older version it hadn't detached yet but I thought that was okay as sometimes I had to shutdown my netbook to detach my Kindle. This time though it
wasn't okay. My Kindle kept restarting until it is started with the original Kindle OS. I've tried to reinstall Flip's Duokan to no avail. I tried Kindle Collections Managers to try and live with the OS but that was a disaster and a half. I tried to download the latest version of Duokan on en.duokan.com but none of the links were working. I finally got the next latest version of Duokan downloaded and installed. Now my Kindle is working again.
So the solution: Upgrade Duokan.
Lesson Learned: Let the Duokan unplug itself before detaching or shutdown the PC to unplug it!
And yes, now I have a phobia against plugging my Kindle to my PC/netbook. 