OK, so the first thing I noticed after moving the content from a sub-directory to the main root was that categories were getting sorted by the ID. Since Uncategorized was the first entry, that was always at the top. It took me a few minutes, but digging into /wp-includes/template-functions-category.php found that the list_cats method had a default sort on the ID column. I changed $sort_column = 'ID' to $sort_column = 'name' and it’s looking a lot nicer.