Okey, I've also posted about my problem over at
Kodi Media Player Options with 3D MVC & HD Audio
and there two friendly users popcornmix & hdmkv helped me solve this issue:
- Open "Settings -> System settings"
- Switch from "Standard" to "Expert" on the bottom
- Go to "Display" Settings
- Enable the Option "Enable Full HD HDMI modes for stereoscopic 3D"
- Enjoy true full-HD 3D MVC content