[-DH-]

Well, "3D not working" ... let's a little more specific on this issue. ;-)
Current version is #1216 on RPi3, I use only .MKV and .ISO files for testing (the samples provided at http://kodi.wiki/view/Samples).
My results so far:
ISO-full3D-sample.iso (plays 3D)

HSDB-3D.mkv (plays 3D)
HTAB-3D.mkv (plays 2D)
3D-full-MVC.mkv (plays 2D)

Renaming the non-working MKV files according the video naming rules (http://kodi.wiki/view/3D) didn't change anything.

So what's the difference of these three .MKV files above:
The working MKV file's video stream has set the flag "Video stereo mode" to "1", meaning side by side/left eye first,
but for the other two files there was nothing.
So I changed both file's video stream flags (using mkvtoolnix/header editor on Windows):
HTAB-3D.mkv - "Video stereo mode" to "3" (top bottom/left eye first)
3D-full-MVC.mkv - "Video stereo mode" to "13" (both eyes laced in one block/left eye first)
... and that fixed it.
So on my end 3D MVC .iso playback is working as usual but all 3D .mkv's need to be tagged properly.