Valve fixed non-Steam apps that would not launch, and two owners say shortcuts now vanish
Valve's October 16 beta client fixes the non-Steam apps that stopped launching after Steam started routing them through Proton on its own, and two owners now report the shortcuts vanishing from their libraries instead. The beta note says "Fixed a bug that caused some native non-steam games to fail to launch", and there has been no stable client release since October 13, so the fix is on the Preview and Beta channels only.
The October 13 stable client carried the Proton default for non-Steam Windows binaries to everyone, and it is still the newest stable release. Image: Valve
What broke first was narrow and specific. The original report, 13736, filed on October 14 and still open with seven comments, says package-manager and Flatpak installs kept working while AppImages would not start at all: "After clicking the Play button in Steam, it thinks for a second and then the button goes green again."
Valve triaged that one the same evening. A Valve member quoted three log lines back to the reporter, among them "Cannot mount AppImage, please check your FUSE setup.", suggested setting the application's compatibility tool to Legacy Steam Runtime, and said it might be a duplicate of a Steam Runtime report about AppImages that has been open since December 2024.
The failure never looked the same on two machines
The reporter's own testing is the best record of how uneven it was. A RetroArch AppImage ran once Legacy Steam Runtime was picked for it, and on a Steam Deck that option only appeared in Desktop Mode, not in Game Mode.
PCSX2 would not launch on Default or on any of the Linux runtimes from 1.0 to 4.0, the report says, and DuckStation launched only on Default. All of them ran from a desktop shortcut or a terminal, which is what pointed at Steam rather than at the applications.
One reporter sees the shortcuts disappear on a Steam Deck as well as a desktop, and the second runs SteamOS in Game Mode. Image: Valve
Two owners describe the same loss from different triggers
On October 17 the same reporter came back with the behaviour on the fixed beta. After the device sleeps and wakes, the report says, any non-Steam shortcut that had been opened before it slept fails and disappears, sometimes with a message about a licence error, and restarting Steam brings the shortcuts back. It happens with AppImages, Flatpaks, plain binaries and Windows .exe files, on a desktop and on a Steam Deck.
A second report, 13754, filed on October 16 by a different owner running SteamOS 3.9.3 in Game Mode on a desktop with a Radeon RX 9070 XT, has the log line. Every launch of a non-Steam shortcut now writes "App 2663220813 marked invalid on platform windows due to not having a common section declaration" to Steam's app-info log, a line the report says never appeared before the update.
What tips it over there is Steam logging on again, whether that follows a sleep or a reconnect in the middle of a session. The shortcut loses its custom Steam Input layout and falls back to the default template, and after a later re-logon it can go missing from the library while the file that defines it still lists it. The workaround given is to restart Steam before launching a shortcut after a sleep or a network drop.
Neither fix has reached the stable channel: both sit in the October 16 Preview and Beta client. Image: Valve
Nobody has answered the disappearing shortcuts
Both reports are open, and the only Valve comment in either of them is that October 14 triage of the original launch failure. The second report has no replies at all, and on the first a repository collaborator who is not Valve offered on October 17 to try to reproduce the original fault. The link between the fix and the new behaviour is the first report's own reading: the comment says the beta update "fixed the initial issue of some apps not launching, which resulted in this new issue of the non-Steam app shortcut disappearing".
The feature underneath all of it is Valve's own. The October 7 beta note says "Windows binaries registered as non-steam games will now run in Proton by default", the change that started routing non-Steam Windows games through Proton without being asked, and the October 13 stable client carried it to everyone. The first report blames that feature for the AppImage regression, calling it a good change overall that "also seems to have broken native Linux non-Steam apps added to Steam".
That stable build has kept Valve's Linux tracker busy. The same October 16 beta note also carries "Fixed Vulkan games hanging after alt-tab", the overlay freeze that had been killing Linux games since that build, so an owner who wants either fix is opting into a beta to get it.
