MKVToolNix Splitting and Joining Stutter
Try using a different video encoder when you create the original file. If that's not under your control, you can file a bug agains MKVToolNix, the author is "always grateful for good bug reports": https://mkvtoolnix.download/ 

Alternatively, try using ffmpeg to join the two parts: https://trac.ffmpeg.org/wiki/Concatenate