If you are using jagtool, you may not see all the EAServer message queues and topics. The EAServer 5.x message service works differently than the EAServer 6.x message service. In EAServer 5.x, the message service is based on EAServer CTS components, while the EAServer 6.x message service uses the JMS APIs. Using jagtool, the only message queues and topics that are visible are the ones that were created in EAServer 5.x using the CTS APIs.
To see all the message queues and topics, use the Management Console. For new development, use the Management Console to create message queues and topics.