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Steam Input remains in desktop mode instead of switching to gamepad mode when running some apps. #10551

Description

@ClaudeLib

Your system information

  • Steam client version (build number or date): 1708985249

  • Distribution (e.g. Ubuntu): Arch

  • Opted into Steam client beta?: No

  • Have you checked for system updates?: Yes

  • Steam Logs: steam-logs.tar.gz

  • GPU: AMD

Please describe your issue in as much detail as possible:

When running certain apps, notably flatpaks but not only them, my Steam Controller keeps emulating keyboard and mouse instead of the virtual gamepad. This was not an issue before the yesterday's update. The affected apps are:

PCSX2, installed from https://flathub.org/apps/net.pcsx2.PCSX2 https://i.imgur.com/I3GHF0c.png https://i.imgur.com/0Z5F3EU.png https://i.imgur.com/PXXb8vo.png
Ryujinx, installed from https://flathub.org/apps/org.ryujinx.Ryujinx https://i.imgur.com/M1dgepO.png https://i.imgur.com/Vblrlqt.png https://i.imgur.com/aNfZGup.png https://i.imgur.com/SOsHRSz.png
Ryujinx, installed from https://aur.archlinux.org/packages/ryujinx-bin https://i.imgur.com/TIMUvNC.png https://i.imgur.com/zpYFsFE.png https://i.imgur.com/OJS0ZpC.png
Toggling "Use Desktop Configuration in Launcher" doesn't do anything.

Some other apps, like https://aur.archlinux.org/packages/pcsx2-latest-bin, or Xenia emulator running via Proton are not affected.
I've also encountered this exact same issue on my LCDeck, it also started happening just yesterday, however running apps from the game mode, rather than desktop mode, seems to help avoid the issue. I can attach logs a bit later if needed.

Steps for reproducing this issue:

  1. Add third party apps as Non-Steam games to the library
  2. Launch them via Steam

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