### 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
}
	if (new_rect == Rect2i(wd.position, wd.size)) {
		return;
	}
	if (wd.xic) {
		
		window_set_ime_position(Point2(0, 1));
	}
	wd.position = new_rect.position;
	wd.size = new_rect.size;
#if defined(VULKAN_ENABLED)
	if (context_vulkan) {
		context_vulkan->window_resize(window_id, wd.size.width, wd.size.height);
	}
#endif
#if defined(GLES3_ENABLED)
	if (gl_manager) {
		gl_manager->window_resize(window_id, wd.size.width, wd.size.height);
	}
#endif
	if (!wd.rect_changed_callback.is_null()) {
		Rect2i r = new_rect;
		Variant rect = r;
		Variant *rectp = &rect;
		Variant ret;
		Callable::CallError ce;
		wd.rect_changed_callback.callp((const Variant **)&rectp, 1, ret, ce);
	}
}
DisplayServer::WindowID DisplayServerX11::_get_focused_window_or_popup() const {