### 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
String ret;
	Window selection_owner = XGetSelectionOwner(x11_display, p_source);
	if (selection_owner == x11_window) {
		static const char *target_type = "PRIMARY";
		if (p_source != None && get_atom_name(x11_display, p_source) == target_type) {
			return internal_clipboard_primary;
		} else {
			return internal_clipboard;
		}
	}
	if (selection_owner != None) {
		
		MutexLock mutex_lock(events_mutex);
		Atom selection = XA_PRIMARY;
		XConvertSelection(x11_display, p_source, target, selection,
				x11_window, CurrentTime);
		XFlush(x11_display);
		
		XEvent event;
		XIfEvent(x11_display, &event, _predicate_clipboard_selection, (XPointer)&x11_window);
		
		Atom type;
		int format, result;
		unsigned long len, bytes_left, dummy;
		unsigned char *data;
		XGetWindowProperty(x11_display, x11_window,
				selection,