### 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
ERR_FAIL_COND(!windows.has(p_window));
	const Vector<Vector2> region_path = windows[p_window].mpath;
	int event_base, error_base;
	const Bool ext_okay = XShapeQueryExtension(x11_display, &event_base, &error_base);
	if (ext_okay) {
		Region region;
		if (windows[p_window].mpass) {
			region = XCreateRegion();
		} else if (region_path.size() == 0) {
			region = XCreateRegion();
			XRectangle rect;
			rect.x = 0;
			rect.y = 0;
			rect.width = window_get_size_with_decorations(p_window).x;
			rect.height = window_get_size_with_decorations(p_window).y;
			XUnionRectWithRegion(&rect, region, region);
		} else {
			XPoint *points = (XPoint *)memalloc(sizeof(XPoint) * region_path.size());
			for (int i = 0; i < region_path.size(); i++) {
				points[i].x = region_path[i].x;
				points[i].y = region_path[i].y;
			}
			region = XPolygonRegion(points, region_path.size(), EvenOddRule);
			memfree(points);
		}
		XShapeCombineRegion(x11_display, windows[p_window].x11_window, ShapeInput, 0, 0, region, ShapeSet);
		XDestroyRegion(region);
	}
}
void DisplayServerX11::window_set_rect_changed_callback(const Callable &p_callable, WindowID p_window) {