Those dropped connections are dropped by the Kindle's firmware. I'm sorry that I didn't had much time lately to look into these issues. But the dropped connections are not really specific to the piece of software, that's due to a daemon that will drop longer lasting TCP connections (except for some special dedicated ports, first and foremost SSH).
I've got to experiment more with SSH tunneling of the VNC connection, which should get rid of the disconnection problem. Well, anyone might give that a try. Forwarding TCP connections via SSH is documented on the Web quite often.