I love this little program and have never had a problem with it. Always choose "go nuts" and it just works. I'm glad they added iPhone support now, I now can memorize family guy on the go.
I think a lot of you folks would benefit from the AppleTV Fooler applescript, which basically creates a wrapper that allows for files to be added to iTunes library without needing to be converted with VisualHub etc.
I recently updated to the latest build of Handbrake. It now converts almost any file as long as Perian and Flip4mac are installed.
Are you suggesting that Handbrake uses Perian and Flip4Mac?
Perian and Flip4Mac are codecs that QT uses and have nothing to do with HB.Well I am not sure. But in older version you couldn't convert .mkv or .avi files. Is the current version you can. Maybe they have a new engine or using external tools like perian.