[Holub]

Here is decision, tested on 4.1.9 and 4.1.11:

find this code in include/categories.php

#
# Gather the array of categories and extract into separated arrays:
# $all_categories, $categories and $subcategories
#
if (($current_area == "C" && defined("GET_ALL_CATEGORIES")) || defined('MANAGE_CATEGORIES')) {
	$_categories = func_get_categories_list($cat);
} elseif($current_area == "C") {
	$_categories = func_get_categories_list($cat, true, "current");
} else {
	$_categories = func_get_categories_list($cat, true, "all");
}

between comments and

if (($current_area == "C" && defined("GET_ALL_CATEGORIES"))

insert

$old_cat = $cat;
if ($current_category["parentid"] != 0) 
  $cat = $current_category["parentid"];

and find

if ($cat == 0)
	$subcategories = $categories;

and insert after

$cat = $old_cat;

You should get something like this

#
# Gather the array of categories and extract into separated arrays:
# $all_categories, $categories and $subcategories
#

$old_cat = $cat;
if ($current_category["parentid"] != 0) 
  $cat = $current_category["parentid"];

if (($current_area == "C" && defined("GET_ALL_CATEGORIES")) || defined('MANAGE_CATEGORIES')) {
	$_categories = func_get_categories_list($cat);
} elseif($current_area == "C") {
	$_categories = func_get_categories_list($cat, true, "current");
} else {
	$_categories = func_get_categories_list($cat, true, "all");
}

extract($_categories);
unset($_categories);

#
# Prepare data for FancyCategories module
#
if ($current_area == "C" && !empty($active_modules["Fancy_Categories"]))
	@include $xcart_dir."/modules/Fancy_Categories/fancy_categories.php";


if (!empty($all_categories))
	$smarty->assign("allcategories", $all_categories);

if (!empty($categories))
	$smarty->assign("categories", $categories);

if ($cat == 0)
	$subcategories = $categories;

$cat = $old_cat;

All done. Just save it and upload file on server.

You will always see subcategories menu (if subcategories exist) in any root category.