I'm having this issue, but only when using content access module. I am using entity relationship 7.x-1.x-dev and views 3.0, content access dev.
I have a topic type and alert type. Alert types reference topic types. The exported view below shows topic content types and uses the "Entity Reference: Referencing entity" so I can get a count of alerts referencing the topic.
When a non-user1 user looks at this view: http://pastebin.com/1BBBeg6j , the user does NOT see all the topics he should. He only see's topics that have alerts referencing them. If the topic doesn't have alerts, it should still show (as it does when using user1) but with a blank in the number of alerts column, but instead that topic just isn't shown.
If I remove the relationship from the view. It will show all the topics to non-user1 users.