I start the game and check MSI afterburner and can clearly see that it does not use the first core of my processor fully. Even if I scroll around and do things that should raise the usage, it never gets above 30 percent. The rest of the cores go up to 100 at times.

Check out this screenshot from when I first start the game:

https://i.imgur.com/aELlqoF.jpg

You can see the first core as low as 9%. The game stutters when I pan around. If I minimize the game and edit the processor affinity in task manager to 1 core and then back to 4 cores, go back into the game, I can see it use all four cores evenly:

https://i.imgur.com/FnfMBZc.jpg

The game then seems to play more smoothly. Is there any explanation for this behavior?

I also took screenshots of Task Manager processor usage without Afterburner as a separate test. (Thinking Afterburner might be causing it.) Same behavior.

Fresh start, then ran around the map a little bit:

https://i.imgur.com/VoCUGkg.png

I minimized the game, went into task manager and changed the processor affinity from 4 to 1 and then back to 4 again. Then I went back into the game. Here are the new graphs from running around the same area. The game felt much smoother to me.

https://i.imgur.com/oMd53lI.jpg

This doesn't happen in any other games that I play.

Tested in Windows 10 Fall Creators Update as well as build 1607
Core i5 4690K at stock speeds
GTX 1080