With Gliffy there are two different plugins: Gliffy for JIRA (Issues) and Gliffy for Confluence (Wiki) which can make it a bit confusing. Depending on what you signed up for, the plugin can be under plugins for Issues and/or plugins for wiki.
If you have the plugin enabled for application in mention and it is not showing up, I would recommend entering a support ticket (support.atlassian.com) so we can take a look over your instance to check everything out.
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