I have a related issue, I just got my KD55XD93 this week and for the first time I'm able to watch 3D movies
Well some 3D movies but not all! KODI detects the movies as 3D, some will be picked up and displayed correctly by the TV whilst others (of the same sbs/tab) format will not, in these cases I get the image twice either side by side or top and bottom. There seems to be an issue with how the SONY TV detects the 3D stream, which as some movies work I can only assume is related to the file itself, however I'm not getting to far in researching if this is controlled by the file header data so if anyone has advice that would be useful.
The action menu on my SONY does not show the 3D option when not using physical inputs or most Android apps, this is a reported problem which SONY seem to be doing nothing about. The work around is to use the SONY TV and Video sideview ios/android app which contains a remote with a 3D button, when activated the TV is forced into the selected 3D mode and the video plays correctly, unfortunately it also has to be de-activated manually at the end of the video. Its a work around you could try perhaps?
I'm more interested however in getting to the bottom of why some films work and others don't... anyone help there?