@BeyondEvil As @ChuckPA has told you, the official standpoint is, that Plex cannot fix intel bugs and the halted development of intel for Sandy Bridge.
Just an idea, if you still want to debug the issue further: please do not experiment with Plex and libva. It’s much more fruitful to experiment with ffmpeg and its h264_vaapi encoder directly and leave Plex out of the picture for now. Please re-encode the files, that produce errors in Plex, with h264_vaapi and also burn subtitles into the re-encode. Then take a look at the result. If it is also broken then there is definitively nothing Plex can do.