Okay so I merged audio and video together in an .mkv file with mkvmerge and there is no stuttering. My only problem is that the audio is .504 milliseconds ahead of the video. I'm guessing it's because the audio track has a few seconds of silence at the beginning. Is there any easy way to fix this?
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If audio has silence at the beginning, the audio would come after the video, not before.
VVV
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You can set a muxing delay in mkvtoolnix to sync it up. Select the stream, format specific options tab, enter the value in the Delay (in ms) box