I have a user who has all rights, including system administrator rights. That user cannot see the Application Links or Application Navigator links in Confluence 5.1. I'm not sure if there's another setting for users that I'm missing. I'd like to link JIRA/Confluence..
Some more digging in logs after I posted this helped my find this article:
Followed the directions and see the links now. It appears that a resource issue with the server is causing some plugins to not load
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