MKV is just a container format. It says nothing about how the video is encoded

Depending on your hardware the one that works super smooth might be hardware decoded, and the other might be decoded in software.

There are various things you can do to figure out their encodings or reencode but anything you Google is going to be more knowledgeable about it than I am

Yeah, 2 different mkv files could have vastly different encoding. Maybe try a different player to see if they okay smoother?

Check both the video and audio streams. I have a 4K movie that the audio defaulted to TrueHD 7.1 and the video was all jacked up after a certain point. Changed to AC3 5.1 and no more issues.

Check my post history if you want, I've dealt with this recently - not sure what device you have but it's a good bet it's a framerate issue. Could also just be what others have said too

Edit: it would be helpful if we knew what hardware you were using