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Audio/Video out of sync. MultiAVCHD transcode 23.976 to 25.000. Why?

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I have a 23.976fps mkv when converted to Blu Ray m2ts using multiavchd, have out of sync video and audio. According to the log file, after the file have been transcoded, the resulting x264 file is 25fps. It then convert it to 23.976fps m2ts. The resulting m2ts has longer duration than the original mkv. I have other 23.976 mkv videos and they converted fine. How can I fix this?
Also is there a way to set CPU priority level?
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I just reencode the video to a new mkv file using MeGUI, then load it in multiavchd, it works. Resulting Blu Ray video and audio is in sync.
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