Whenever I boot up Sekiro it doesn’t register my controller unless I unplug the keyboard first. Is there a way to select controller without having to unplug the keyboard?
Do you saw this behaviour with other games also?
Out of games I own and have tried the controller with, yes. It wouldn’t work with Descenders but I only played the trial of that. Works fine with Nioh and Dark Souls 3. It also works fine with PCSX2 and RPCS3.
Do i understand you right, that this quoted games works flawless with the controller. Without the need of unplugging your Keyboard?
Yes, that is correct.
Thats sound like there are a few games that shows a higher priority to force your Keyboard.
No experience here around this problem, other people can probably help you better than i do.
Maybe the priority is USB Port(if you use USB on both devices) related? I would try to swap this ports with the devices. 
Do you use something that could be related to this unequal device priority?
Maybe steam game launch commands for the working games or non working games?
Or maybe different proton version which maybe lead to the different device handling. 
Good ideas, I’ll have to experiment around with the USB ports. Thank you.
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Did you solved it?
Nope, not yet!