I have no idea why is this happening, but sometimes, part of configured controls reset to unassigned (most of movement controls and half of the rest). Does anyone have this issue? And most importantly, does anyone know how to stop this from happening?

No, as a regular user. I'm using Windows 8.1. I have googled this problem, apparently only one user in steam forums reported same problem. Even though, he claims that controls reset, every time he goes in the menu, in my case they can reset even without it. The most frustrating part, is that sometimes (just like now), "restore controls to the default" option doesn't work, most of the controls still remain unassigned.

Same thing here. Just started playing and couldn't jump. Then i realized that a few actions just aren't mapped. Restore defaults doesn't work. Some ideas to fix this?

Happend to me too. After restarting the games some functions where unassigned to a key. So I had to do this again with every restart.
After some time the problem was gone. Dunno why and how.

I know this post is old, but I had the same problems with controls and graphic settings not saving, as well as not being able to save the game. I couldn't find a solution anywhere so wanted to share what I did to fix it for me.

Windows Security was blocking folder access. I had to go to Windows Security > Virus & threat protection > Protection History, and there I saw several "Protected folder access blocked" by FEAR.exe for folder "%userprofile%\Documents". All I had to do was hit the drop and select "Allow on device" and fear.exe was now able to save my settings.