[hdmkv]

That "bug" is present in kodi on all platforms... Every 3d iso played in 2d stops at some time. This on windows, android, openelec.
Not only with seamless branching titles...
Remuxing doesnt help.
I tried that.
All those titles do play fine on himedia, total media theater, powerdvd... I tried it on mede8er too and that want a problem either... So it is kodi somehow..

So, had to try this. Played ISO of 'Finding Nemo 3D' & skipped ahead to 1h26m15s and plays fine via my RPi2. This was in 3D mode. Stopped, and re-played, now in 2D mode to 1h26m15s. Still no issue. However, mine's a movie-only ISO made via tsMuxeR (main H.264/MVC video stream, TrueHD audio stream & chapters only).

Playing fine just past 1h26m15s in 3D mode (photo taken with 3D glasses in between iPhone & screen):


Playing fine just past 1h26m15s in 2D mode:


Did discover another issue while doing above tests though, with my Epson 5025UB projector. I had been relying on its 'Info.' tab to see what framerate it was receiving from media player, but looks like this can't be relied upon for 3D ISO's... they all show as 24.00 for RPi2 and HiMedia Q5. Switch to 2D mode, and PJ shows 23.97. Don't know if this means true 23.976 is being displayed or Epson converts to 24.00 or what?!?! Wish there was a reliable, affordable device available to test true framerates.

Oh, one more thing... I'd previously reported RPi2 may not be able to handle very heavy action sequences in 3D ISO's. This was because when I (two separate times) played 'Avengers: Age of Ultron' 3D ISO, the opening action-packed sequence had frame skips & stuttering. This time, after the 'Nemo' tests above, guess what?! Smooth playback. I'm discovering that with my Synology NAS, I need to play a couple of random videos (preferably high bitrate test files) when I initially fire up my home theater & use any media player to fully wake everything up (if that makes sense). Seems the initial skips/stutters may be related to the hard drives in the NAS not being fully spun up. Cuz even the high bitrate Jellyfish & Birds clips play a little better after initial runs.