This is known to happen when your user account does not actually have the "Portfolio for Jira user" permission. More details in the Permissions in Portfolio for Jira.
By default the groups 'jira-software-users' and 'jira-administrator' will tend to have this permission. However if you have removed those groups, or your user account is not a member of the groups granting this permission, you can see only that administration menu.
The good news is that, if you're seeing that, you are probably an admin account that can give yourself the needed permissions to view this. If you click that Administration link it should take to your a page such as /secure/PortfolioPermissions.jspa
From these add a group that contains your user to the "Portfolio User" permission and that should immediately let you see more options from that navigation menu.
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