On your frontend site, the category tree is cached to help improve loading time. When you make changes to your category tree, like adding or removing categories, the cached category tree on your site won't always reflect these changes. To fix this, you can perform a cache bust on your site by adding the following text to the end of your frontend URL: ?force=true.
For example, if my frontend site was http://testccsite.crystalcommerce.com, I would go to http://testccsite.crystalcommerce.com?force=true to update my category tree. Even though you are going to that URL in your own browser, it will update the categories on your site for any customers browsing it as well.