To clarify, you're getting _content_ spillage by the sound of it? I take it the two sites don't look exactly alike (and e.g. in their respective /etc/nginx/sites-enabled/ files, it's "server_name <actualURL>;" not "server_name _;" for instance)?
If you add a test description on one site say, does a search on it (e.g. in quotes content in the description you create like "An Oct 25 test description") show up in both? As in, by Archival Institutions do you mean http://<site>/repository/browse shows the same two institutions even though one site should not have the second one?
Or do most things not spill over, but some do (for example, if you go to Admin -> Settings, pick site information and on one site modify the Description and then refresh both sites does the change happen on both?
Hope those questions made sense - let me know if not.
Dave Hume, Artefactual Systems Administrator