Observing the log entries in smps with these warnings : ACEAGENT: The message entry does not exist for Message ID: 1001
R12.8.X Policy server.
Reasoning : This usually happen when there is response delay's at RSA side. Once the Policy server services are stopped all the Policy server handles using the RSA authentication which are stale state are closed gracefully. This is not the issue with Policy server side.
Policy server services restart has resolved the issue.
Here is the RSA KB article describes the reasons for the delays from RSA side.