Check out this thread
What you want to do is exactly what is described further down in the above thread. Create a new “root” category and save it (make sure its enabled. Then go into manage stores and in your store choose your newly created category as that stores root category.
Then you create new subcategories to your new “root” category and again make sure they are enabled.
Basicly you need one level of subcategorys to have them displayed at your store as the first level doesn’t “belong” to the navigation.
My guess is due to fact that you can have multiple setup of categories in multiple stores and thats why you need to define one top level of category first
Hope this helps