In Jira 4.1 and earlier, when you added a Trusted Application link to Confluence in Jira, it by default knew that the trusted URL's should be /plugins/servlet/streams, /sr/jira.issueviews:searchrequest, /secure/RunPortlet, /rest, /rpc/soap.
Now in Jira 4.3, when you add an Application Link, the replacement of Trusted Applications, by default Incoming Authentication is neither enabled nor when you enable it does it have any trusted URL's. You have to go search around on Google or find an old Jira instance to figure it out.