I had some issues when I tried configuring my controller to be more similar between games. I struggled for quite a while trying to get Valheim working properly again. I believe the fix that finally did it was turning off Xbox Configuration Support in the Controller Settings page (bullet 3 in this page: https://wiki.albany.edu/display/icehcspace/%5BSteam%5D+How+to+set+up+a+controller+for+any+PC+game)

I also deleted the controller settings directory in my local steam configuration (somewhere under AppData), but it wasn't completely fixed until I turned off the setting mentioned above.