I have this problem too with the native version, if I run it with proton it works but I want to play the native version.
Wanted to comment saying that I too had this issue with a Dualshock 4 today, but forcing Steam Input to be disabled for Dead Cells seemed to work. Right-click Dead Cells, Properties -> Controller, and set Override for Dead Cells to Disable Steam Input.
Hope that helps someone!
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Your system information
Please describe your issue in as much detail as possible:
Native Dead Cells game won't recognize my Xbox One S controller. Other games like Hollow Knight work just fine. I have tried both default setting and "Forced off" modes of per game controller settings.
I have also tried removing libSDL bundled with the game with no success either.
Here are some logs of Steam controls and terminal outputs:
Terminal_output
Controller_UI
controller_log
Steps for reproducing this issue: