--- resolved via a PM ---
It's likely that neither the file nor VP is at fault. The viewer apparently handles the file differently than Videopad.
Load the clip into the bin. If not prompted for a stream, right-click it and Select Stream.
Again load the same clip into the bin and select another stream. Drop it onto the overlay track, immediately above the first clip.
Hide one of the video tracks. Or UNlink and delete it, if you'd rather not see it.
If this icon isn't visible, right-click at the left of the track and make the Hide choice.... 
Now you have a single active video track and two audio tracks, each with its own stream.
Upload and share your file and we will confirm that this works correctly in version 12.30, which it does here when tested on a multi-stream MKV file.