Gliffy Project and Gliffy Diagrams for JIRA are designed to work in tandem, and Project does include some elements of Gliffy for JIRA. Because of this, installing both plugins will result in 2 Gliffy links.
If you observe two Gliffy buttons, please check to see whether you currently have Gliffy for JIRA installed. If so, uninstalling Gliffy for JIRA should resolve the issue, causing only one link to show.
To ensure Project functionality, be sure to uninstall the Gliffy for JIRA plugin, and not Gliffy Project.
If the issue persists, please reach out to Gliffy Support, and we'll be happy investigate further.