Does the Agile button come with an arrow? Do you see any options like Manage Boards when clicking on it? Or do you see any warning/error message?
You may go to Administration -> Add-ons -> Manage add-ons and see whether JIRA Agile is installed and/or enabled.
How's everything? Are you sure the version of JIRA Agile is compatible with JIRA 6.1? You can refer to this and update accordingly. Other than that, if you can see the boards, I think a re-indexing of JIRA will help.
...PermissionsStartOnly=true User=www-data Group=www-data ExecStart=/opt/jira/bin/startup.sh ExecStop=/opt/jira/bin/shutdown.sh TimeoutStartSec=120 TimeoutStopSec=600 PrivateTmp=true [Install] WantedBy...
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