OK, I've tried what you suggested by moving a category to the "root" area. However, when I do this I get the error "category does not exist" and the category is moved under "Home" and can not be deleted or modified. I attached some ss of what I'm talking about along with a snap of the sql database categories. I'm really trying to figure this out, I want to delete that stupid category "Front and Read Stands" on the home page.
Here you can see that "Front and Read Stands" were moved to the "Root" Dir, but I still got an error
http://gpmotoparts.com/pics/Category_no_exist.jpg
I also tried to create a new category in the root level.
http://gpmotoparts.com/pics/new1.jpg
As you can see, it puts it right under Home/Home
http://gpmotoparts.com/pics/new2.jpg
Last screen shot is of mysql database where you can see the Home is the top level category.
http://gpmotoparts.com/pics/mysql.jpg