I wrote this on the Steam forums, it's not a fix but a workaround, requires a second and trusty game pad. http://steamcommunity.com/app/282350/di ... 885227260/
This is what I do and it works fine, don't get me wrong, there is a bug with this and it's top priority that it gets fixed.
So online games disables your game pad, we all know that, but I have two game pads plugged in so the first time I found my controller wasn't working I jumped for the other one and that one was working fine. So the bug moves your primary controller to your secondary, if you don't have a second game pad plugged in it will fall on the keyboard, if you only have a keyboard it will fall on an alternative keyboard profile.
The very successful workaround is to have a second game pad and switch to it for online, it hasn't failed me yet.
I know most of you probably don't have a second game pad just lying around and working fine, but it has worked flawlessly for me and I thought it could help a few of you.