If your Steam Controller configuration doesn't work in a game, it may be because the game doesn't support the style of input you've chosen. Browse through community configurations for that game and see if one works.

Gamepad-only input styles will only work with gamepad supported games.
If you're playing a game that doesn't have gamepad support, like DOTA 2, you won't be able to use gamepad-only input styles, 'Joystick Move' and 'Joystick Camera', to move or look around.

Flexible input style commands must accommodate game limitations.
Flexible input styles, 'Directional Pad' and 'Button Pad', give you the choice to allocate a keyboard, mouse or gamepad command to a button. If you choose a gamepad-specific command, like a Y or X button, this input will only function properly in games with gamepad support.