The "Site Map" is a product of your fso template, since Dokuwiki doesn't use a 'site map'. But it does show a table of contents, which refers to main headings on your current page and not to other pages on the wiki. How headings are displayed is controlled by the toc settings in the configuration manager (see
http://www.dokuwiki.org/config under 'display').
It's possible that the fso template has changed some of the default settings for the table of contents, so that it doesn't display correctly when you are using the default template.
I would start with a fresh install of Dokuwiki to see how it works; then when you install your fso template you will know where their differences are.