I have a Samsung D8000.
In my experience always was needed to identify the device under the section "Media Receivers", the same with my Samsung Bluray player BD-6500. Doesn't matter the version of the firmware. My TV came with version 1015 and now the last is 1023.
For both devices it is mandatory to select the option "Samsung TV" in order to play any mkv file. If not the device displays "unknown codec" and refuses to play.
I have purchased twonky for mac and I am very happy with it!!
Because of my good experience I decided to move my media server to a brand new Linksys E4200 with twonky embedded. (My plan was to turn off my Mac)
options are blocked in the E4200 and I cannot access the config page to select the right device (Samsung TV), so I cannot play mkv.
Now I am back to my Mac waiting for a fix.
Tell me if I can collaborate doing some experience with my Tv and Bluray.