In stand-alone Confluence, with an Application Link built to stand-alone JIRA, where the Application URL is different from the Display URL, the link in the Navigation Bar to go to JIRA incorrectly uses the Application URL, rather than the Display URL.

In JIRA, the same link built the same way pointing back to Confluence uses the Display URL - which is the desired behavior.

In our environment, both JIRA and Confluence are behind an SSL terminator - they can talk to each other without SSL, but users cannot reach them on the same ports they use to communicate with each other (both have two entries in servers.xml, and are listening on two ports each). This seems to work great in every respect except for the link on the Navigation Bar from Confluence to JIRA.