I have this too, on two of my themes. On my other themes the plugin is fine.
1. Bluesky theme http://www.geektofreak.org/ duplicate first post on home or category pages
2. Bluesky theme http://www.paulthompsonsblog.com/ duplicate first post on home or category pages
WordPress 3.1.2.
Bluesky 2.1 by Elegant WordPress Theme
