Regarding invisible application windows. It has to do with monitor configuration changing. I can reproduce it, when I disconnect my monitor from my notebook. Afterwards the invisible application windows occur when I start XWayland applications.
There is also an issue for mutter. Version 48.3.1 fixes the issue on my side, allthough others report that they still have problems.
nvidia + wayland + gnome
Same behaviour here with Signal, pcloud (AUR) and p3x-onenote (AUR).
I switched to X11 for the time being, as I am dependend on the last two, and everything is working fine.
Will probably test the electron adjustments mentioned here later today:
https://wiki.archlinux.org/title/Wayland
Better try mutter V48.3.1 from unstable (see my post before).
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This fixes it for me, thanks for the heads up.