I would guess that the OSD menu doesn't show well also...
Even if you watch the movie correctly, you should select the type of 3D video in the 3D Menu... And it's even trickier...
In my installation/skin, when I play some 3D movie (generally SBS) and Kodi doesn't recognize it (mainly when they are online streams that aren't named acording to
Kodi naming conventions for 3D videos) I have to manually select the type of video.
The issue is that in the OSD menu, the 3D submenu is grayed out, so I have to go to video settings, change 3D mode from Auto to something (SBS for example). This, doesn't put Kodi in 3D mode (OSD menu still shows only once and not twice as it should for 3D SBS stereo), but at least activates de 3D mode sub menu.
Then I go to that 3D submenu in the osd and select again SBS.
After that kodi changes to 3D mode (I see 2 osd menus) and I can change my TV to 3D Mode and subtitles work perfect...
Maybe this works for you, maybe not. But it's worth trying.
PS. I'm not on latest versions nor standard skin so some of this stuff might work differently in you setup.
