First, there were a bug in the version 11 SR1 that had this behaviour. That was fixed in an updated release of version 11 SR1 (11282 and higher), if that's your case, you better upgrade to QlikView 11 SR2.
Make sure the documents have the proper security configuration: Settings menu, Document Properties, Opening, Strict Exclusion. If not, the user is able to open the document in any case, regardless whether or not they have some data related to them in the data model.
Anyway, feel free to post an example of your section access here.
Hope that helps.