In SharePoint 2010, if you save a site as a template and create a new site based on the saved template, the navigation settings of the new site may not be identical to the navigation settings of the site that was used as a template. For example, in the original site that was saved as a template, certain navigation items that were created as a "Heading" will appear as links on the new site. Similarly, if you have configured certain navigation links to open in a new browser window, the setting is not retained when the site is saved as a template.
This behavior is by design in SharePoint 2010. The navigation settings are not packaged into the template when a site is saved as a template. As a result, the new site that is created from the template will not have the navigation settings identical to the original site.
In the new site that has been created from the saved template, manually change the navigation node settings to get the desired behavior. This can be done by navigating to the site settings page from the "Site Actions" menu, and clicking on "Navigation" under the "Look and Feel" section.
Save site as template; Navigation settings