Controller support is straight up broken :(

When you boot up the game, it will "double detect" mouse and keyboard and controller inputs and require double confirmation of start up EULA agreements and brightness adjustments. It keeps waffling back and forth between controller and m&k. You can go to the options menu and choose controller only as an input, but then the controller doesn't work at all. When you restart the game, it goes back to the first issue. Please fix Larian, this was a promised feature, thank you.

EDIT: Solved my own problem. Be sure disable any Steam controller templates you used during the early access period.