I have the Apple MPEG-2 playback component installed, and the latest version of Perian. I've noticed that if I use MKVMerge on the same input file, the output video is fine. One solution was to use MKVMerge to merge the video from the VOB file with the audio, subtitles and chapters from the MakeMKV file.
MKVMerge tells me that the format of the MakeMKV-converted video was V_MPEG2 while that of the original VOB was MPEG-2. Don't know if that means anything.
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MakeMKV v1.5.2 beta darwin(x86-release) started
Debug logging enabled, log will be saved as /Users/jamie/MakeMKV_log.txt
Optical drive "BD-ROM OPTIARC DVD RW AD-5670S 2AHH" opened in OS access mode.
Opening files on harddrive at /Volumes/LaCie 500GB/DVDs/South Park 2/201 Not Without My Anus/VIDEO_TS/
Title #0 was added (5 cell(s), 0:23:28)
Operation sucessfully completed
Saving 1 titles into directory /Users/jamie/Desktop
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
Program reads data faster than it can write to disk, consider upgrading your hard drive if you see many of these messages.
1 titles saved