I think I have some useful tricks to share with you to play MKV in VLC beautifully without hassle.
Solution 1: Change Parameters
If the MKV file that is skipping is playing from a local hard drive, choose the "All" settings at the bottom of the dialog to show all of the options, then navigate to Input / Codecs -> Access modules -> File.
The caching value here is set in milliseconds, so setting the value to 1000 will buffer for 1 second (the default is 600, or 0.6 seconds). The problem with setting this option too large is that if you want to manually skip to a new point in the file, there will be a larger lag while the content is buffered again.
Solution 2: Disable hardware decoding
Some users resolve choppy VLC Playback on mkv files by disabling hardware decoding. Normally you would want hardware acceleration of the decoding process, but in some cases, it can conflict with your drivers, and it is worth a try.
Solution 3: Find VLC player alternative
Media Player Classic is a compact media player which serves as an alternative to VLC player for Microsoft Windows. For Mac users, you can try MXplayer.
Solution 4: Convert MKV to VLC most friendly format
Since MKV can't be supported well by VLC media player, an ultimate solution is to convert MKV to VLC most friendly format. Brorsoft Video Converter is the utility for you. With it, you can fast convert MKV to AVI that can be easily played in VLC.