Sounds like your controller might be using direct input instead of XInput. Is there a setting for it? What controller are you using?
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Old Xbox one controller, wired switch pro controller Wii mote and some off brand game cube controllers
The xbox controller should work but the other ones might need a program to translate them to Xinput. Either way check your Steam input settings, I think you can try to register and remap your controller there.
I'm guessing you're on Linux, right? And is Steam installed through flatpak or your OS's package manager?
I'm asking because I wonder if Steam has installed some dependencies that aren't available system-wide. I know on Debian based distros you generally want the steam-devices package installed which provides a lot of compatibility for various controllers.
Windows user actually I have been thinking about transitioning to Linux but I haven't gotten around to it