Have the Site Map match the Catalog Organization structure

I have a site where there is a category which contains sub-categories. Those sub-categories are currently displaying in the Site Map under the --Root Category-- along with all the other categories. I would like those sub-categories to be listed ONLY in the category to which they belong. Those sub-categories are currently listed twice (once in the --Root Category-- and once in the category in which they belong). I think this behaviour is confusing for our clients when they use the site map as they are seeing the same products listed in two separate locations. The Site Map should match the structure of the Catalog Organization.