MKVToolNix garbled segment transitions on playback...

[takeajustin]

Hi all. I have a new 4K that contains both theatrical and uncut versions. Rather than having both cuts as two separate files, they laid out the m2ts files as segments that kind of jump between each other during playback. I tried combining them in mkvtoolnix and though it worked, on playback the video gets all pixilated and garbled during those cut/uncut transitions. What might be causing this and can it be fixed? Maybe I was doing something wrong when combining them...?
Thanks for your help.

[Ennio]

This way of authoring is called seamless branching. From such discs, you can best demux your desired version(s) with DGDemux. Once done, import the resulting elementary streams in MVKToolNix to mux to mkv.