I have a site with 2 document libraries that are identical. When I change one the other is updated. When I add a document to one it is added to the other. This site collection was created from a site that I exported and imported into the root of a blank site collection.
Using SharePoint Manager, do they show up as the two different doc libraries or do you just have two different links going to the same doc library? Do they have different guids or the same guid? Do they have different urls?