The latest version of vfe.sh (2.0) allows you to select whether the script will run the transcoding commands using an 'ffmpeg' or 'avconv' command. The default is ffmpeg, and it's the kind of thing one is likely set and leave, so I have added a 'converter' value in my .vferc file. On my Mac I'm using ffmpeg, and on my Ubuntu machine avconv. With avconv I found that Ogg encoding was sensitive to the audio bitrate, and that 128 was a good value. At any rate, it is now a setting that you can adjust on the command line or in your .vferc file. Lastly I added more explicit output so that you can now see in the terminal the full form of the command that the script ran for each video type.
Updated files are on: