I know this is an old thread, but the issue still persists trying to work with a 1080p60fps .mkv file. I tried using Shutter Encoder's rewrap (aka remux) function, and the same thing happened. The resulting mp4 file ended up being VFR. The only two viable solutions for me currently are:
1. Using Handbrake with either Production Max or Production Standard presets. This results in an MP4 file.
2. Using Shutter Encoder with any of its editing codec presets. Results in a gigantic .MOV file.
So far, Handbrake seems like the better option for me being that I'm only looking to apply some light cuts and edits (via Premiere Pro) to a 30 min game footage file and then upload to YouTube. I don't need the world's best-quality file, but even with a 7GB original MKV file, it's quite a bit of a dramatic wait until the file finishes processing going either route mentioned above. The final edited file won't be as large of course, but it's definitely a process to get a workable file with no hiccups due to the VFR in an editing software.
It would just be so much easier if I can use remux directly in OBS, but I guess it is what it is. I'm not sure if there's been any other updates on this front, so I thought I'd ask here.