### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
DisplayServer *ds = memnew(DisplayServerX11(p_rendering_driver, p_mode, p_vsync_mode, p_flags, p_position, p_resolution, p_screen, r_error));
	if (r_error != OK) {
		if (p_rendering_driver == "vulkan") {
			String executable_name = OS::get_singleton()->get_executable_path().get_file();
			OS::get_singleton()->alert("Your video card driver does not support the selected Vulkan version.\n"
									   "Please try updating your GPU driver or try using the OpenGL 3 driver.\n"
									   "You can enable the OpenGL 3 driver by starting the engine from the\n"
									   "command line with the command:\n'./" +
							executable_name + " --rendering-driver opengl3'.\n "
											  "If you have updated your graphics drivers recently, try rebooting.",
					"Unable to initialize Video driver");
		} else {
			OS::get_singleton()->alert("Your video card driver does not support the selected OpenGL version.\n"
									   "Please try updating your GPU driver.\n"
									   "If you have updated your graphics drivers recently, try rebooting.",
					"Unable to initialize Video driver");
		}
	}
	return ds;
}
DisplayServerX11::WindowID DisplayServerX11::_create_window(WindowMode p_mode, VSyncMode p_vsync_mode, uint32_t p_flags, const Rect2i &p_rect) {