I've never seen a MKV file play 2 audio tracks. This can occur with AVI files though. To correct the issue, go to the AVI TAB and set Haali as the AVI splitter. After doing so, when the file is playing, there will be a whitish icon in the system tray that can be rightclicked and allow audio track selection.
As for the LiveTV stutter, when selecting to use the [x] SUGGESTED settings checkbox, current releases (4.0+) of my software will ask you if you're a LiveTV user and make settings according to your answer to the question.
Check in Control Panel | Sound, under your active connection to see that you have set the proper speaker count. My software picks up on this setting and uses it to setup audio output from the installed codecs.
Please know, Media Center playback is only affected by settings made in the 64bit app. All other players are affected using the 32bit app.
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