MKV files. How do i convert them?

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Hi I have a vista media center 64bit, and have tried to run mkv files on it. Without decent result. When i play them, the picture quite often stops and jumps. And the the sound is concequently out of sync. I have used Combined Community Codec Pack, and have also tried with the 64bit version af k-lite codec pack. (required to get mce to play mkv at all. If not installed, mkv files can only be played from wmp) I have no trouble playing any other HD file formats as .ts, wmv-hd, or dvd-ms HD But my question is, how do i convert the mkv files, to something i can play? I have looked around for ages now, and found that vlc player can re-encode. But the only result is, no picture, only sound. I have also tried a program called Super. But i just get more confused when looking at that GUI. How do i set it up to convert to .ts format? Anyone here who can help me to convert my mkv files.