Not an explanation or proper fix, but running the games through Gamescope might fix it by side effect. In gamescope the game would never lose focus and so shouldn't have problems resuming afterwards.
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Disclaimer: Theory, based loosely on related experiences in Windows ages ago back when I actually used Windows.
The keyboard handler might be getting confused when you Alt+Tab, leaving the game stuck thinking you're still holding Alt+Tab when you return to the game.
Just for shits and giggles, the next time you experience this, try tapping Alt once or twice to see if that refreshes the keyboard buffer and status.
You might even try tapping the other toggle/special keys as well, such as Ctrl, Shift, Esc...
I realize Windows and Linux are like comparing bananas to oranges, but still, the keyboard buffer might not be getting refreshed properly when switching apps.
It's worth a try, do let us know if this helps in any way.
This has happened to me when playing older games on Linux
Sounds plausible.
FWIW, New World (doesn't have borderless fullscreen) got me into the habit of tapping the Windows key before doing anything outside the game. Other than when the game is starting, it never has any problems when I do that.
I'm using EndeavourOS, KDE, Wayland, so YMMV.
sudo dmesg -Tw
Try opening the Nvidia control panel, turn off Force Composition Pipeline. I had this same issue.
Might be game specific. I don't know how to solve the issue but maybe you could try opening the game in a different virtual desktop and switching desktops and see if that causes it. Or press the meta key and see if that causes it too
Most probably graphics / nividia issue. But not a general issue, related to the configuration or hardware or something.
For most such cases when you can't figure out anything, it's generally a good idea to ask in your distro's support forum. There are people who can usually help you debug a few things. It doesn't always solve your problem, but you can get some possible pointers.
It could be a game issue. I remember a lot of games had issues with alt-tabbing back when I used windows. It could also be a Wine issue. I had one game that started freezing when alt-tabbing after a Wine update a couple months ago. Rolling back to the previous version fixed it.