I basically only have a few ontologies loaded. I loaded foaf and skos ontologies into their own named graphs, no data yet. Regardless of how I set up my database, I seem not to be able to get named graphs out. That is why I was wondering if there was some setting that was conflicting with getting named graphs out.
Got it, I was using pystardog to load the database and I was using <urn:graph:skos> to load the data. There <> was causing the trouble. Removed those and it worked.