Don't have an exact answer,but if your article matches a percentage of keywords as used in another article, it will sometimes be categorized as duplicated. Example; I wrote photography articles for another online web organization before I switched over to Hubpages. Some of these articles were very similar to the ones on Hubpages, therefore some of my hub articles came up as duplicated.
Contact the Hub pages support staff and present your argument for clarification as you make a strong point and seem to have done your homework by using copyscape.
Sorry that this is the best answer that I can give you at this time.