### 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 (XGetWindowProperty(x11_display, x11_window, desktop_geometry_prop, 0, LONG_MAX, False, XA_CARDINAL, &type, &format, &geom_len, &remaining, &geom_data) == Success) {
								if ((format == 32) && (geom_len >= 2) && geom_data) {
									desktop_valid = true;
									long *size_data = (long *)geom_data;
									desktop_rect.size.x = size_data[0];
									desktop_rect.size.y = size_data[1];
								}
							}
							if (geom_data) {
								XFree(geom_data);
							}
						}
					}
					
					if (desktop_valid) {
						Atom desktop_viewport_prop = XInternAtom(x11_display, "_NET_DESKTOP_VIEWPORT", True);
						if (desktop_viewport_prop != None) {
							unsigned long viewport_len = 0;
							unsigned char *viewport_data = nullptr;
							if (XGetWindowProperty(x11_display, x11_window, desktop_viewport_prop, 0, LONG_MAX, False, XA_CARDINAL, &type, &format, &viewport_len, &remaining, &viewport_data) == Success) {
								if ((format == 32) && (viewport_len >= 2) && viewport_data) {
									desktop_valid = true;
									long *pos_data = (long *)viewport_data;
									desktop_rect.position.x = pos_data[0];
									desktop_rect.position.y = pos_data[1];
								}
							}
							if (viewport_data) {
								XFree(viewport_data);
							}