I had this same issue. I had installed ffmpeg via RPM (with yum) but that version did not include the –enable-libvorbis etc…
Actually an additional symptom was that empty files would appear in the destination directory.
I fixed it by following these instructions to remove the RPMs and compile from source – now it works perfectly:
http://cumulusclips.org/docs/install-ffmpeg-x264-on-centos/
I also needed to grab libvpx to finish, instructions here:
http://ubuntuforums.org/showthread.php?t=786095&highlight=Upgrading+FFmpeg+x264&page=149
Great plugin, thanks Kyle!
Greg
