The search_engine templates are meant to complement (and actually require) the default templates. As soon as you click "Main Index" in the search engine templates (or any of the other links at the top), you are taken out of the default templates and the last unread feature will work perfectly. These templates should be installed in admin/templates/search_engine. The .tplinfo file is important as well - it tells the template parser than any files not found in the search_engine templates should be pulled from the default template set.

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Jason Rhinelander
Gossamer Threads
jason@gossamer-threads.com