I think the issue is how the games are programmed. Some games check which controllers are plugged in only at start and some do regular checks during runtime.
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I've sometimes had this bug on Bazzite, but it seems to be game-specific when it happens.
While I've had some nagging KDE session issues, thankfully using an xbox controller has thus far been a great experience for me in Bazzite. On Windows I had to replug my dongle after every. single. freaking. reboot.
Hope you get it sorted soon.
Same thing happens to me with an Xbox controller plugged into my PC with a USB cable. If it goes to sleep, I need to restart the game to use it again. And sometimes it suddenly stops working and sends a constant "analog stick down" command until I unplug it (which means I can't use it anymore lol)
Is it wireless?
Yes, bluetooth. The controller is seen again by the OS and then by Steam but not by games already started.
I'm betting this has to do with your OS settings for two things:
- Bluetooth device sleep settings
- ID mapping for BT devices
If X minutes lapses without activity, your OS may put some device and device controllers to sleep, like USB and BT devices. Install 'powertop' and look to the tunables tab to see which has which.
I would also have a look at the deviceid of the Bluetooth controller while it's working, and then check again afterwards. I think you can use 'bluemon' as an easy tool for that, but whatever works. If the ID changes, then it's possible steaminput isn't paying attention to it.
Depending on your OS, you may have to install some compatibility tools for Steam as well. On Debian-based, it's called 'steam-devices', but there are others that work as well. See the Flatpak section here: https://wiki.archlinux.org/title/Steam about 'steam-devices'.