Thank you for the post.
The FileMaker Server 12.0v5 (Advanced) update was released to resolve this issue. More from the article linked above:
"The FileMaker Server 12.0.5 update uses the JAR manifest file attributes introduced by Java Runtime Environment 7, update 45 (JRE 7u45). The FileMaker Server 12.0.5 update adds the permissions attribute consistent with Oracle’s security recommendations.
Without this update, FileMaker Server administrators will see the following warning message when opening FileMaker Server Admin Console or the Deployment assistant: "This application will be blocked in a future java security update because the jar file manifest doesn't contain the permissions attribute. Please contact the publisher for more information.""