MKVToolNix and yes. My specs are probably just not up to par.
Btw, Kitt is the person I have been talking about.
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?