@jsl21: I just downloaded today's paper, and I got every article listed in the index. Are you comparing to the same index at
http://www.nytimes.com/pages/todayspaper/index.html?
I believe that the ads are being skipped correctly, so I'm guessing that the problem you're experiencing is something else. It could be that some articles are being updated at the time you're running the recipe, or something else causing a connection failure during the download of that article.
Take a look at the download log to see if there's any further information there.
I'll keep poking around. It's possible that I'm just not getting any ads at this time.
G