I am led to believe that CloneDVD is causing the upside down image and not the Nokia Internet Tablet Video Converter.

Since the new version was released several days ago, I'm happy to say that it has worked fine for me, with output videos playing flawlessly on my N800. I just converted all 6 episodes of Star Wars overnight and am copying them over to my N800 now. Input files were 700MB, output files were 569MB

if only I had somewhere to backup these converted videos....say, like an FTP server or something.