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Have you tried MPC-HC with the CCCP codecs? It uses GPU acceleration and runs 1080p mkv videos off my 4870 just fine.
I watch mkv's on a computer with the following specs and get no choopyness at all:
Win xp
P4 3.2ghz
2 gig Ram
4650 gpu
I use VLC to play my mkv's you most definetly do not need to download a mixture of codecs etc..... vlc is adequate for 95% of your media playing.
Check you harddrive space if its still choopy. Give you machine a disk defrag too.
It just occured to me, that the choppyness is most likley to be your hard disk.
Either something is accessing the disk whilst you are trying to watch your movie, or you do not have enough ram/hard disk space.
If your using vista.... well then the answer is the self evident.
Visa has an anoying habit, of churning the hard disk when the computer is not active.
If its xp or win 7 and its still choppy ...
If your comoputer specs are more than mine ( p4, 2 g ram and 4650 gpu) and you got plenty of hdd space etc...... then you might benefit from wiping your comouter clean and reinstalling operating system.
Make sure you got the latest drivers for your gpu as well.
But honstely vlc is more than adequate for watching mkv's, I do it all the time.