FontAgent appears to not auto-activate font despite all attempts to remedy the issue with standard troubleshooting, 

Possible cause: When an application launches for the first time after the auto-activation plug ins are installed the alert below is presented.

Some customers are alarmed by this dialog and click Don’t Allow. After this is selected, permissions will not allow auto-activation to function, and the system will not present any communication as to why that occurs.

To fix this the user needs to go to System Preferences>Security and Privacy>Automation and check the checkbox below the effected application. This action sets the permissions for the FontAgent Auto-Activation plug-ins to function as expected.