### 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
_THREAD_SAFE_METHOD_
	ERR_FAIL_INDEX(p_shape, CURSOR_MAX);
	if (p_shape == current_cursor) {
		return;
	}
	if (mouse_mode == MOUSE_MODE_VISIBLE || mouse_mode == MOUSE_MODE_CONFINED) {
		if (cursors[p_shape] != None) {
			for (const KeyValue<WindowID, WindowData> &E : windows) {
				XDefineCursor(x11_display, E.value.x11_window, cursors[p_shape]);
			}
		} else if (cursors[CURSOR_ARROW] != None) {
			for (const KeyValue<WindowID, WindowData> &E : windows) {
				XDefineCursor(x11_display, E.value.x11_window, cursors[CURSOR_ARROW]);
			}
		}
	}
	current_cursor = p_shape;
}
DisplayServerX11::CursorShape DisplayServerX11::cursor_get_shape() const {