I have a PN59D550. but I understand the issue is with 2010 samsungs too.
If I encode a 2.35:1 ratio 3D Bluray into a half-sbs file with black bars cropped, lets say 1080x814. If I play on Samsung player and turn into sbs mode, it forces the display into mode 2. the picutre is stretched and proper aspect ratio is lost. I need to encode the movie with black bars included (not cropped) in order for the samsung player to display properly.
This is not an issue for 2D movies. I can crop the bars, set the player to mode 1, and no stretching is applied, it plays at proper aspect ratio, black bars are at top and bottom, but I didn't need to waste bitrate encoding black bars. this is how it should work.
I can play cropped half-sbs files with other external players and everythign is fine. The problem is only with the samsung player. In 3d it forces you into mode 2.