The artboard setup of documents has any number of problems, worst of which is the inability to simultaneously configure document setup, guide, guides, and other attributes for multiple artboards in a document. Copying such settings between artboards would also be useful, including artboards in different documents.
Also, Document > Setup: Margins is currently buggy when applied to an artboard. Making changes results in bizarre behavior, with inaccurate margins being set, or margins disappearing entirely. When making changes, it's usually necessary to set all margins to zero, close the dialog, then reset them them to the desired values.
Thanks,
Bryan