After 15 hours across 2-3 days, controller stopped working in Totori. Steam's "Controller input setting" window pops up in the bottom right corner but doesn't work. Tried plug in/out, still nothing.

Tried previous game Atelier Rorona that I finished just before starting Atelier Totori and in that one, it works fine.

EDIT: Tried to play with Steam controller setting. Possible last Steam update did something with it, right now it works again.