I had the same problem the first time I connected after getting the kit. I searched around and didn't find any mention of this problem, so I'm glad I'm not the only one 🙂
Here's what I think I did to try to fix it. It now syncs properly, and I don't know what parts of this caused it to work:
1. Restored my iPod - it was brand new, so I didn't lose much. I was hoping that this would force iTunes to ask me for my account info again, but it never asked.
2. Opened Safari (disabled PithHelmet, because it was preventing the site from loading), created a Nike+ account, logged in, and I think there was a setting somewhere that I set to tell it to remember me
3. With the browser open and logged in, I connected my iPod with data from a "fake" 5 second workout on it (just to have something to sync)
4. Told iTunes to sync the data
5. Told iTunes I wanted to Visit the site
6. On the webpage that it pulled up, I logged in as myself
7. All of my runs since then have synced up!