Did you get a brand new Copy of 6, or did you do the upgrade from an earlier version?
When I went to register my C6 after upgrading from C5, I got the same error message. However, when I checked my “Show Registered Products” in MySteinberg, it showed Cubase 6 as the registered “Cubase” product on my eLicenser, and not Cubase 5 as before. So, I am thinking that if you do an upgrade, and if your eLicencer is already registered with your MySteinberg account, it automatically updates when you install Cubase 6.