Mkvmerge drops frames on certain m2ts files at the start
If a bluray m2ts stream starts with a timecode that contains 0x47 it will resync to that instead of the real sync byte. This results in output files missing a few frames at the start, till it resync with the proper one again. ffmpeg also shows this behavior but tsmuxer or DumpTS and (makemkv) can output files that have the entire video intact.
for reference the patch i wrote https://gist.github.com/jsaowji/fa589a61fd7d81e0b449865e417dcc7e
In the meantime I also found another opensource project that ran into the same issue in ffmpeg based software their investigation and fix can be found here: