The “Remember Window Position” setting is not present in the Windowed Mode settings on Linux. Moving the window around and resizing it does not persist between relaunching or even loading a different game.
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Are you on Wayland (note for other readers, Wayland is the new windowing protocol that replaces Xorg)? Because Wayland does not support persistent position between relaunches. It works on X11 though.
As a workaround with KDE: If you are using KDE, then you can at least force a specific position by setting up rules. But this is then always the same position and won’t get updated when closed. I just tested it. If you don’t use KDE, then not sure if your window manager has implemented this.
I am using X11 with Cinnamon.
Hmm, maybe it remembered on my old system due to some personal setup. Looks like RetroArch supports Remember Position only on Windows platforms. I tried to research and at least since 2021 there is this post: https://www.libretro.com/index.php/retroarch-1-9-8-released/
The PR also cleans up the Settings > Video > Windowed Mode menu, auto-hiding options where required, and re-initing drivers when toggling Remember Window Position and size. Also, since the ‘remember’ part of Remember Window Position and size is only enabled for Windows, an alternate Use Custom Window Size is provided on other platforms.
At least this is the state in 2021, I don’t know if it changed since then. On my system with Wayland+KDE I don’t have this Remember option as well.