The newest version is whatever you can dl from tunebite.com it really is a small small download so I suggest just reinstall if you're not sure.

I really REALLY suggest you use tunebite and advanced MP3 Converter ( it works the best for me ) the Converter keeps the tags on but it will not sort it into folders but it's really easy to manually do that if you can see the tags already.

Tunebite will never get you a 1gb song miles long, it gets the track duration from windows media player and only cuts off +-1 second at the very end because of absolute silence ( 90% of the time it is exact duration ).

Use the default Vorbis encoder.

Edit: One thing for all people to know, your Virgin Digital Method will eventually be fixed they will never ever beable to fix tunebite or any other program like it.