The way to fix this is from your Steam Library page, right click on the game and select "Properties". Go to the "Controller" tab. Click the underlined "Controller configurator," click the official controller selected (has a '>') and then navigate to the "Community layouts" tab. From there, there are multiple controllers you can select. I used John's. Select it, then apply settings. This should fix it.

This method works in a lot of games if you have a controller issue or you want better settings for your controller. It is invaluable if you ever try to use a gyro controller.

I hope this helps.