[Atreyu]

It has already been mentioned mkv is just a container.
To progress, we need to find out the characteristics of the problematic formats.
MediaInfo might give some insights.

I have had issues like this one the past.
In my case, all files that were created with a specific version of Handbrake combined with variable bitrates caused very similar symptoms.

[Derek]

Have you tried a clean portable install and PatK is correct I had a badly outdated advancedsetting.xml with lots of irrelevant settings in it and some that were causing slowdown and even crashes (some time ago mind you) but always worth starting from a portable install pure clean and see what happens. also try 16.0 as well as 16.1

Also as said above try software as well as DXVA as if you have a pretty nippy machine you'll not notice much difference speed wise but quality comes next once your actually up and running. .