I understand that you need to re-bind unwanted keys to something else rather than clearing them: if they're cleared, the game will try to "fix" them be reassigning them their default values next time it starts. The solution is to assign them to something you'll never use, which apparently fixes it ("apparently" as I haven't tried it myself).
This does not always work. As I've reported in the past, some keys keep resetting regardless. For example, I keep reassigning Q/E to control the camera, but every time I restart the game, E once again opens the character screen (as well as swirl the camera, at the same time).
And in his example, he rebinds X to Sneaking, just to see X rebound to some GM option upon restart.
