Yes, the absolutely are! You can 100% use a Nordstrom gift card at NR. I've used Nordstrom gifts cards at the Rack many, many times. Where did you see that you can't use the gift card at the NR? I see on the NR site that you can't use Nordstrom Notes online there yet, but I always use my Notes at NR in person. ETA2: Sorry, just noticed that you tried to use it online at NR. Maybe they're not set up for that, just like with Notes? Strange. You'd think they'd have worked that out.
ETA: http://shop.nordstrom.com/c/gift-card-info