It appears that NEF has been sending the wrong scope bases freqently lately. I got two standard bases when I ordered my Ultra barrel plus an extra Ultra base, and I've seen lots of similar mistakes posted here.
I think the guy at the factory that used to strip the but pad screws got transfered to the scope rail dept, and now he's screwing that up too.
Don't worry, the only advantage of having the Ultra rail is that you can mount your scope further forward because the rail is longer. The extra set screw is just something that can cause problems down the line, and it serves no real purpose. I kept my standard rail and never looked back.