Hi!
I can confirm this too!
I'm using Libreelec 8.2.0.1 on a Raspberry PI2.
As BastiB said just 3D ISO files are affected, I tested with many of them.
When I choose the "same as video" 3D mode it switches to SBS automatically.
If I ssh into the Pi and issue "tvservice -s" while playing one of them I get:
state 0x12000a [HDMI CEA (32) 3D FP RGB lim 16:9], 1920x1080 @ 23.98Hz, progressive
Indeed my 3D tv seems to detect and behave accordingly to the FP mode of the MVC stream but again it is wrongly set to SBS mode by Kodi.
Again, as BastiB said no problems at all with MKV 3D files (full MVC files of course), for instance this MKV 3D sample file: drive.google.com/file/d/0BwxFVkl63-lETWMzM1dRZF9XMDA/view from the official kodi wiki (kodi.wiki/view/Samples) works fine.
The reply to the "tvservice" command is exactly the same but this time the 3D is correctly set.
While for instance this other ISO 3D sample (always from Kodi samples) presents the same problem described above: ISO-full3D-sample.iso - Google Drive
NB: to make this last ISO 3D sample recognized as a 3D file I need to edit the name into something like "ISO-3D-full-MVC" so that I'm asked what kind of 3D I prefer, and choosing "same as video" enables the wrong SBS with FP mode.
Thank you very much!