|Jira Agile 6.3
Per the JIRA Agile documentation, setting an Epic issue's Epic Status field to Done should omit that Epic from the Agile Board. However, one or more projects do not appear to follow this rule.
To ensure you're facing this specific problem, try each of your Epic Status options to determine if any of them cause the Agile Board to omit the Epic card.
This is caused by the way that the Epic Status field is checked by the Agile Board. When checking for done-ness, JIRA Agile identifies the option that is last in the list as the definition of done.