Resolution: Usually it seems to be a permission issue. Check the JMSADMOPTIONS.ini and the servers.xml. The default admin username and password seems to conflict somehow when it's different from the ones used in servers.xml. Modify JMSADMOPTIONS.ini to make the default username and password the same as that used in servers.xml.
To do this in the builder, go to Tools>Options>TIBCO EMS Admin>Admin Tab or manually.