The decoders in these Smart TVs are not as good as your PC. I don't want to repeat that discussion but will share I've had some luck with HANDBRAKE. And again, sorry but this is not an offer to write any tutorial on HANDBRAKE.
There's another issue looming and there is no fix. Some models stop playing and 2 hours and some number of minutes. Some think this is to curb the play of pirated movies.
I have a samsung 40f5500 and when i play movies from my external HDD most of the movies plays well but for some movies it stops saying some error msg and gives option to either skip or stop.
Many a times by manually forward also help to play movie but its irritating too much.
Is there any application to use any other external app to play the movies from external hdd or any other way to repair those mkv files for smooth playing of media.