This document focuses on the issue of protected sites and pages not showing data in Google Analytics.
Users of protected intranet sites will not show data in Google Analytics. Also, pages that are locked down to a Manifest Group or to all NetIDs will not show results in the pulled dataset. The reason for this is that Google's bot will not have access to crawl your site content if it is password protected.
This is a known issue and no simple workaround is currently available.