### 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_
	if (p_mode == mouse_mode) {
		return;
	}
	if (mouse_mode == MOUSE_MODE_CAPTURED || mouse_mode == MOUSE_MODE_CONFINED || mouse_mode == MOUSE_MODE_CONFINED_HIDDEN) {
		XUngrabPointer(x11_display, CurrentTime);
	}
	
	bool show_cursor = (p_mode == MOUSE_MODE_VISIBLE || p_mode == MOUSE_MODE_CONFINED);
	bool previously_shown = (mouse_mode == MOUSE_MODE_VISIBLE || mouse_mode == MOUSE_MODE_CONFINED);
	if (show_cursor && !previously_shown) {
		WindowID window_id = get_window_at_screen_position(mouse_get_position());
		if (window_id != INVALID_WINDOW_ID) {
			_send_window_event(windows[window_id], WINDOW_EVENT_MOUSE_ENTER);
		}
	}
	for (const KeyValue<WindowID, WindowData> &E : windows) {
		if (show_cursor) {
			XDefineCursor(x11_display, E.value.x11_window, cursors[current_cursor]); 
		} else {
			XDefineCursor(x11_display, E.value.x11_window, null_cursor);