### 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
++event_index;
							event = next_event;
						} else {
							break;
						}
					} else {
						break;
					}
				}
				last_timestamp = event.xmotion.time;
				
				
				
				Point2i pos(event.xmotion.x, event.xmotion.y);
				
				bool filter = false;
				
				if (xi.state.size() && Vector2(pos).distance_squared_to(xi.mouse_pos_to_filter) < 2) {
					filter = true;
				}
				
				xi.mouse_pos_to_filter = Vector2(1e10, 1e10);
				if (filter) {
					break;
				}
				const WindowData &wd = windows[window_id];
				bool focused = wd.focused;
				if (mouse_mode == MOUSE_MODE_CAPTURED) {
					if (xi.relative_motion.x == 0 && xi.relative_motion.y == 0) {
						break;