I am having the same problem with Article Bot. I have been manually removing them. I believe the problem lies within changes of the RSS feed.
For example, SI.com adds advertsiments to their feed, once ArticleBot grabs the ad, I physically delete the post. If you browse in the rss_cache directory (phpmyadmin or other sql database tool) you will see a list of all threads, including the duplicates. which leads me to believe something (url maybe) was changed on the rss side.
It hasnt become a nuicense YET, but I am still looking for a better way to manage duplicates.
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