Drupal, version 4.6.6, with this patch applied, and TripSearch running generates two hits per word in 'search_index', one of type flexinode and one of type node.
This results in duplicate search results for each node.
I do not believe that this is a flexisearch or flexinode issue, rather a search module issue, but I am documenting it here so that: (1) It is documented, (2) people can find it (it's likely that others may have the same issue). I'm also leaving it open as I look into it and I've assigned it to myself (though help would be nice).
At this time, it's a strange inconvenience.