Run Tools->Recalculate Hyperlinks and see if that makes a difference.
The unlinked files report shows all files that are not linked to
directly from the home page. "Directly" means a link in the form <a
href="pagename.htm">text</a> (or <img src="picturename.gif"> or similar
for images), any pages linked to only by javascript or server side
scripting are included in the unlinked files report.
There are columns in the report that show how many pages link to each
"unlinked" file, and how many pages those files link to.
Are the navigation bars you are using based on FrontPage navigation? If
so, in Navigation view, do the pages actually connect with the Home page
which has an icon resembling a house on it?
