Resolution:
If EMS FT is running active (primary) and standby (secondary) servers, then the Admin operations (either using tibemsadmin tool or the Java Admin API) should be limited to the active (primary) server only. Separately reconfiguring the standby server can cause it to overwrite the shared configuration files and unintended misconfiguration can result.

Example, one should not create queues and topics on a standby EMS server:

1).  Start a FT pair of EMS servers.
2).  Connect to the active server from the tibemsadmin tool and create a queue “queue.test1”.
3).  Send 5 messages to the queue queue.test1 .
4).  Connect to the backup server instance from the tibemsadmin tool and create a queue called “queue.test2”.
5).  Now failover the EMS server and do a "show queues".
6).  The queue queue.test1 as well as the 5 messages it contained are dropped.

Also, since the primary EMS server is locked the store files and the secondary EMS serer does not have access to the store files.  The"read only" inquiries, like extracting the count of pending messages etc., should be performed only to the active server because the results from the secondary server are always incorrect.