Just wanted to say I have the same issue.
I use a VIX image (latest update) on a Vu+ Duo2 and I can see most of the 3D movies correctly.
On a couple of movies, I can see only 1 side of the movie in 2D - instead of the two side-by-side.
Up until recently, the 1 side was not resized, it was displayed in the middle of the screen with a black region all around.
In the last update, the 1 side is stretched / resized to use the entire screen.
Based on your post here, I've looked for a tool to allow me to edit the MKV file and change the "frame-packing" attribute but I couldn't find one.