Ok, guys... As Patrick Oberli stated before (thanks, Patrick!), now I think we really isolated the culprit.
Actually the problem surfaced two times for me, even after the latest updates and all.
And what made it work again (without the need to logoff/login) was to CLOSE STEAM. Yep, it seems Steam is the great evil boss here. :P
So, please, try this within your systems and tell me how it goes. After closing Steam you could turn on the controller again and the bug should've went away (even launching steam again, turning the controller off and on most of times seems to work, you should
need to close it only sometimes).
"Recently" Steam launched a new functionality that takes over the xbox controller anywhere in the OS. You could even control the mouse cursor with it (if properly enabled in the Big Picture mode), and probably this is the main problem and what is causing
this bug, even when the functionality is disabled.
Please, give us your feedback so we could make sure the culprit really and finally is Steam and other people could come here and try this temporary fix as well.
Edit: I was thinking here... if it still doesn't work, maybe it's a combination of the new Creator's update and closing Steam. Worth a try, if you ask me...