Videopad will detect some multi-channel audio streams and prompt for choice. See this thread...
http://nch.invisionzone.com/topic/25410-videos-with-multiple-audio-tracks/
When it doesn't run the file through this tool, which should extract independent files to load into VP.
To see if others get the same result, please upload your file, make it shareable (public) and post the shared link here.
You can also submit a bug report by clicking the chevron at the top-right of the VP window.