The issue from the log files...

To perform the agent user authentication, it instantiates the AuthContext by requesting to OpenAM on what it actually needs (hence the authContents.getRequirements())

If the login is successful, then OpenAM will setup the SSOToken. The code however never gets that far though because the exception is thrown with the string value of 'Unable to get Application SSO Token'. Therefore when this issue occurs, it's not even completing the AuthContext, which implies to either the credentials being incorrect or that the service name is unreachable/unavailable.

From my side, I eliminated the credentials because this was an initial installation of the agent, which requires the agent profile username/password.

My statement is also supportive based on the return response, 'Failed to create new Authentication Context: Cannot find server ID'. One way to test the service name is accessing the /namingservice URL of your OpenAM instance. For example, http://servername:8080/openam/namingservice. This should bring back something such as 'OpenSSO', which is the identifer you require for the AuthContext initiation. If you're sitting behind a LB with multiple instances, then ensure that the naming service is also available.

My issue was actually related to the server in which it tries to access the naming service. Within the OpenSSOAgentBootstrap.properties, you should be able to locate the 'com.iplanet.am.naming.url' value pointing to the namingservice value. I altered this value to be pointing to the LB instead of the designated server that was SSL enabled and not the open port directed to the single instance
#com.iplanet.am.naming.url=https://server1:8080/openam/namingservice
com.iplanet.am.naming.url=https://loadbalancer:443/openam/namingservice

Once I did this, I was able to progress with the initiation of newly deployed J2EE agent.

I returned back to this thread because I was receiving the same, 'Caused by: com.sun.identity.security.AMSecurityPropertiesException: AdminTokenAction: FATAL ERROR: Cannot obtain Application SSO token' error
however the stack trace presented a different error. In this scenario, it was 'Check AMConfig.properties for the following properties' followed by 'com.sun.identity.agents.app.username'
and 'com.iplanet.am.service.password' values.

I confirmed (repeatedly) the credentials within the properties file as well as the agent profile was correct though I was still receiving the same error

Even though the agent was pointing to the sub-realm, the root domain has an agent that was exact to the one within the sub domain. Removing the agent from the root or changing the name from within the sub-realm will resolve the issue

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