Win Intel HTPCs/NUCs & Kodi-native 3D MVC Playback
"Mainline" Kodi does not support MVC playback (will just play back one of the images and ignore the other, which is what you are getting with your tests), so you are a bit stuck I think

See if anyone else can give you any advice here, but I think you are out of luck.

Only other thing I can think of is there is another modified version of Kodi called Kodi DSPlayer (see 223175 (thread)) which uses a different built in player to play the videos in Kodi. I know this also supports 3d (although when I last used it a while ago, it was a bit inconsistent for this; the MVC builds just work). You might want to give that a go - maybe it is possible to change the output to SBS (I don't really know).
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Messages In This Thread
What about xvYCC / x.v.Color - by ma9ick - 2016-04-15, 14:01
June 30 download link broken? - by CooperCGN - 2016-08-02, 08:18
RE: Intel HTPC/NUC's w/reliable Kodi-native 3D MVC Playback - by woronczak - 2017-01-02, 07:56