I'm having the same problem. I just went to start a new game and look, what happened with me is I set the level scaling on then changed to a different difficulty while in the menu. It resets the selection to none. Not really a bug from the look of it but a rather small oversight. But I would really like to be able to enable it mid game, I'm getting a bit over leveled but I really don't want to start a new game if I don't have to.
My worry is that it's something that needs to run from the start, like changing the challenge mode of Divinity 2 - it loads the game from the beginning with it in place and can't be changed later. But I looked at the difficulty options closely and it doesn't mention that it can't be changed once the game begins like the expert mode or path of the damned (the highest difficultly.)