MKVToolNix Splitting and Joining Stutter I've been trying to split a tv show episode into two seperate parts, but whenever I try to rejoin the split files, I get a pixelation look on the merge locations.

I've been using MKVToolNix to try and do the splitting/joining.

I made an example of the problem I am having.

https://i.imgur.com/2V35u2B.gifv

Right as the credits start you can see the screen blips grey, and then after that some of the credits become pixelated also.

Is there anyway to fix this problem and just have one smooth video?
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