I have tried 15 videos now and every one works perfectly.
In the 3D options for the youtube video you want, select:
NO GLASSES
then PARRALEL,
then Swap right-left (or it will be reverse 3D on the 3DS)
Next just copy the URL into the program and start the conversion.
clicky: http://gbatemp.net/topic/315456-youtube-downloader-and-3ds-co...
