One problem with mine was the audio syncing: notably while the admiral is mocking Vader’s religion
I just checked that point and they were both in sync. So I’m not sure what caused your problem, but I am pleased that it doesn’t appear to be an inherent problem of mkvtoolnix. 😄 But certainly yes makemkv beta will also perform the job wonderfully, and there are certain types of video streams that it handles better than mkvtoolnix when joining together from branching. But as this was an audio problem and not a video problem, and as x264 would be one of the best streams supported for joining, that’s unlikely to be the problem.