If upgrading from a version before 0.6.0, read the following:
Old command strings are no longer valid in this version, as {tempFileOutput} does not exist anymore. To update to the new settings, do File > Settings > Load preset and load the new default.ini
Along with the new command strings, the default video output is now .mkv and not .avi for better compatibility with all audio codecs (when I tried avoiding re-encoding audio before, FLACs wouldn't work with .avi, but they do with .mkv)