I was excited to see that Mp3Tag has added support for Matroska, thanks for that! I finally had the chance to test it and I am encountering some off behavior.
I found that it would not record my changes in some files. It appeared that removing the entire tag first and then adding data back works, but that was only partially true. I honestly can't seem to get things to work the same way every time. I have seen situations where the tag panel would not update the file, but using the edit cell function in the file list would, but that was not consistent. So far my tests have been restricted to the Title, Artist, Album, and Comment fields.
I'm not sure about MKV, or if this is relevant for it or what the OP is encountering, but when outputting to MP4 in video encoders there's an option to 'optimize for web' (alternatively named faststart in ffmpeg), which places the video metadata at the start of the file IIRC which speeds up reading the video info when streaming over the net/viewing in the browser but prevents the metadata from being edited the same way unless you re-process the entire file. At least, that what I recall last I spoke with someone when asking about the option.
Thanks for this. I tested it and it worked perfectly. Not sure what SeekHeads are or why they cannot be expanded, but I can probably live without that.