I'm not an expert in anime, but I heard that OP/ED are often encoded with different frame rate (constant, not variable, but different).
There's an unknown muxing problem with some mkv's now. The resulting mkv generated with ffmpeg is somehow broken - this's why I asked about manual remuxing in MKVToolNix.
Remuxing, just opening the transcoded file in mkvtoolnix and then remuxing it, it works normally so far. So that's great! Thanks!
I'm wondering though, since the mkv only contains one video stream, how can some parts of it have a different framerate, when it's listed as constant? Or rather, how can i go about it to find out if that's the case. ffmpeg and MPC-HC doesn't seem to show that anywhere.