Here is what happens:
Example:
'News' is category id 1 and sort order 000.
'CMS' is category id 2 and sort order 001.
'Wordpress' is category id 3 and sort order is 001-000.
This will display 'Wordpress' as a sub-category of 'CMS'' which is right.
After adding a new category and move it as a sub-category, 'Wordpress' has still the sort orderof 001-000, but is now displayed unter 'News'.