### 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 (rect.grow(-1).intersects(workarea_rect)) {
								rect = rect.intersection(workarea_rect);
								XFree(workarea_data);
								return rect;
							}
						}
					}
				}
				if (workarea_data) {
					XFree(workarea_data);
				}
			}
		}
		
		Atom client_list_prop = XInternAtom(x11_display, "_NET_CLIENT_LIST", True);
		if (client_list_prop != None) {
			unsigned long clients_len = 0;
			unsigned char *clients_data = nullptr;
			if (XGetWindowProperty(x11_display, x11_window, client_list_prop, 0, LONG_MAX, False, XA_WINDOW, &type, &format, &clients_len, &remaining, &clients_data) == Success) {
				if ((format == 32) && (clients_len > 0) && clients_data) {
					Window *windows_data = (Window *)clients_data;
					Rect2i desktop_rect;
					bool desktop_valid = false;
					
					{
						Atom desktop_geometry_prop = XInternAtom(x11_display, "_NET_DESKTOP_GEOMETRY", True);
						if (desktop_geometry_prop != None) {
							unsigned long geom_len = 0;
							unsigned char *geom_data = nullptr;