The frame rate variable (VFR) is a common problem, mainly with anime video.
To solve the problem you need
mkvtoolnix installed in your system and:
1) Extract the timecodes of video track from your source mkv file:
"...megui\tools\mkvmerge\mkvextract.exe" timecodes_v2 "source.mkv" 0:"timecodes.txt"
Or use some GUI for mkvextract, for instance with
UsEac3to:
- Load your source.mkv
- Click over Auxiliary Tools -> 'MkvExtract/Mux'
- Select 'Extract Timecodes of Track'
- Select the video Track and 'Run'
You obtain a "source.mkv_0.txt" file at same folder than "source.mkv"
2) Recode your source.mkv with MeGUI to output.mkv
3) Open output.mkv in MkvToolnix-gui.
- Select the video track
- Load the timecodes.txt in Properties -> Timecode file
- Start muxing