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You're using XWayland, the X11 compatibility layer for Wayland, which is known to be a bit funky at places.
For the time being I'd recommend running the editor in single-window mode, either through the --single-window CLI parameter or the relevant editor setting interface/editor/single_window_mode.
There's also an experimental native Wayland backend1 which might give you better luck (or not :P) but note that it has still some limitations, like single-window-mode only for now (I'm trying to work on it but I'm quite busy lately).
Tested versions
System information
Godot v4.3.stable - Debian GNU/Linux 12 (bookworm) 12 - Wayland - Vulkan (Forward+) - integrated V3D 7.1.7 - ARM Cortex-A76 (4 Threads)
Issue description
Whenever I have a 3d scene open (even a blank one), the menus and sub-windows have a graphical glitch. I've attached a couple images.




Steps to reproduce
Absolutely no specific project is necessary. Just start a 3d scene and open a menu or try to add a node.
Minimal reproduction project (MRP)
N/A
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