I’ve just made two MKVs, one with mkvtoolnix and the other with makemkv (so I can see the results). Can you give me a specific example of a problem with yours? It is certainly possible that mkvtoolnix is having difficulty joining together certain types of tracks while maintaining interleave points perhaps that’s the source of the problem?
One problem with mine was the audio syncing: notably while the admiral is mocking Vader’s religion and while Porkins says “I’m right with you Red 3”. There were other places but those two pop in mind. There were also horizontal video tears sprinkled throughout, ranging from minimal to very offensive. Those varied with each export, however.
You should try out makemkv. It’s free, easy to use, and I’ve only had great results with it.