exactly what is happening to me. i dont think you do something wrong. i assume its the program and jrk190 might have only tested 2D-videosI tried it, but no luck but it may have something to do with the video i downloaded
I DL'd a vid from youtube using the side by side option, then converted it using your tool,
the video was converted then when i played it in the 3DS, it was also side by side. lol
i Dont know what I did wrong.