It might have to do with permission settings. Are you running the game as administrator?
What OS are you using?
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.