If you are having problems with your controllers responding correctly in Steam run games, it could be that you haven't set up your Steam client to support your controllers.
Before doing this, please make sure:
No other Bluetooth devices are connected
No other controllers are connected (USB or blue-tooth)
How do I set up Steam support for my controller?
Unplug any controllers you have plugged in
Launch the Steam client and click the icon at the top right to enter Big Picture Mode
Go to Settings
Then select Controller Settings
Make sure that the support for the controllers that you're using is all On
Then simply plug in your controller and retest the game!
Please also make sure your General Controller Settings are set correctly:
Launch the Steam client
Click Steam > Settings > Controller and press the "General Controller Settings" button and make sure that "Playstation/Xbox/Generic Configuration Support" etc are all toggled on.
Then simply plug your controller back in and retest the game.