As sleekgreek said, it's to do with the tags in the mp4 file.
the framepacking tag needs to be set to 3 for SBS L&R movies. it's either 4 or 5 for top and bottom, but i can't remember for certain.
You can use videolan's X.264 encoder to do that. but that only puts out H.264 video, so you'd need to then use something else to do your audio and then combine them again into one mp4 container.
the command for x.264 is:
Code:
x264 --frame-packing 3 -o [Input].mp4 [Output].mp4
but like i said, this is video only, so remember to use whatever other tools you use to encode the audio and then recombine.