So, when you say "subcategory," do you include subforums with subforums of their own? My forum has a lot of nested forums, and I just did a test run of the converter, and none of the nested forums were copied at all. I got my parent categories, the main forums under the categories, but no child forums below that.
None of my "1st tier" subforums are category objects, but all of them have children of their own.