I’ve read through some threads regarding Kodi and 3D movies even on an LG TV…
I’m using a Nexbox A1 fully current and the latest Kodi 17 release candidate. I’m playing movie files in 3D format on my LG TV (55LA6900-UD).
Playing regular movies appears to be fine (not as touchy I guess) but playing a 3D movie (either OU or SBS), when I enable the 3D on my TV, the two images are not lined up and are out of whack by like a couple of inches.
The kids wanted to watch a 3D movie and that was my first test and it was like this. Strangely enough, if you stare at it long enough your brain will line the images up until you look away… 
Anyway, after that I tried several troubleshooting items:
I can play the same movie from VLC (outside of Kodi) and the two images are lined up perfectly when I turn on the TV’s 3D mode.
I tried leaving all the video calibration settings at zero and changing the TV display mode (just, zoom, etc…) No change.
I tried using the video calibration in Kodi to get the screen correct but still no change.
At no point or Kodi configuration did changing the TV display settings help. However, in some cases (with zeroed out video calibration) the TV couldn’t even figure out which 3D mode it was being displayed in (OU or SBS).
One thing that did seem to help was the setting to minimise the black bars. At maximum setting (20%) the image out-of-whack was cut in half (an inch instead of 2 inches). But that’s the highest you can set that setting.
One thing I am considering trying is going back to Kodi 16.1 and seeing if that helps at all. The only reason I went to Kodi 17 was to resolve bluetooth headphone issues I was having with Kodi 16.
Anyone have any links, experience or suggestions that might help?
Thanks!
-TimG