Google Web Master Tools shows lots of duplicate title tags (and duplicate meta descriptions) because there are two versions(?) of every page/link almost - with the only difference being .html at the end of the link.
How would these pages of been created by CS Cart? Obviously I've only created one instance manually. Somewhere, a second page has automatically been created. It seems to be something CS Cart used to do, but now doesn't as only products created before a certain date (I can't pin the date down exactly) and therefore possibly a certain update?
Example - Earpods have been on the site since inception.
have you tried to insert canonical tag to every main pages ? My website has showed alot of duplicate too, but it put canonical on top of the page and it's gone.