### 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
mm.instantiate();
				mm->set_window_id(window_id);
				if (xi.pressure_supported) {
					mm->set_pressure(xi.pressure);
				} else {
					mm->set_pressure(bool(mouse_get_button_state().has_flag(MouseButtonMask::LEFT)) ? 1.0f : 0.0f);
				}
				mm->set_tilt(xi.tilt);
				mm->set_pen_inverted(xi.pen_inverted);
				_get_key_modifier_state(event.xmotion.state, mm);
				mm->set_button_mask(mouse_get_button_state());
				mm->set_position(pos);
				mm->set_global_position(pos);
				mm->set_velocity(Input::get_singleton()->get_last_mouse_velocity());
				mm->set_relative(rel);
				last_mouse_pos = pos;
				
				
				
				
				if (focused) {
					Input::get_singleton()->parse_input_event(mm);
				} else {
					
					
					
					
					
					for (const KeyValue<WindowID, WindowData> &E : windows) {
						const WindowData &wd_other = E.value;