I have Splunk Enterprise 6.1, I've had the same issue on 6.0, and Enterprise Security 3.0 running. I pull in a datasource like normal and everything is looking good until I create tags and field aliases. If I create them in the Search and Reporting app, or any other as long as it is not ES, and I share them globally with everyone having read permissions ES does not see the tags. I can search in any app other then ES and the tags work. If I search inside the ES app context with the same search as before it does not produce any results. The field aliases have the same behavior as the tags when searching.
