The order of objects within a folder can be adjusted so that the navigation is as desired.
This is the only place in the CMS where you will not have to submit.
If the navigational order doesn't change, first check the index block to verify it is set to order by Folder Order. Secondly, if some of the folders or objects aren't visible, they may be set not to be included in the navigation. In the example below, the _cms, css and the imx folders that come with the site are set to be invisible in the navigation.