### 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
XEvent &peek_event = p_events[p_event_index + 1];
			
			
			
			
			
#define ABSDIFF(x, y) (((x) < (y)) ? ((y) - (x)) : ((x) - (y)))
			::Time threshold = ABSDIFF(peek_event.xkey.time, xkeyevent->time);
#undef ABSDIFF
			if (peek_event.type == KeyPress && threshold < 5) {
				KeySym rk;
				XLookupString((XKeyEvent *)&peek_event, str, 256, &rk, nullptr);
				if (rk == keysym_keycode) {
					
					++p_event_index;
					_handle_key_event(p_window, (XKeyEvent *)&peek_event, p_events, p_event_index, true);
					return; 
				}
			}
			
		}
		
	}
	
	k->set_pressed(keypress);
	if (keycode >= Key::A + 32 && keycode <= Key::Z + 32) {
		keycode -= int('a' - 'A');
	}
	k->set_keycode(keycode);
	k->set_physical_keycode((Key)physical_keycode);