I'd be keen to know what the issue is too, as I use MKVToolNixGUI to cut and/or join MKVs regularly without any problem.
DanDare1983,
If you open an MKV with MPC-HC and navigate with the keyboard left and right arrow keys while holding down the shift key, you'll jump between keyframes.
When you're at the appropriate keyframe, use the Navigate/GoTo menu (CTRL+G) to get the frame number. Use it when cutting with MKVToolNix (split after frame number). Of course there's no guarantee there'll be a keyframe where you want to cut. Sometimes there is, sometimes not.
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