I'm having this problem in a major way, on a Network site. Most of the sites sort-of behave with the odd dupe, but 2 sites in particular have gone absolutely bonkers to the stage where I've had to write a script to delete dupes after FWP's cron run while I investigate. I'm getting several dupes of each posts, often more than a dozen of each.
The settings on all sites appear to be the same, however a colleague has noticed that these 2 sites seem to differ ever so slightly, with _synfresh appearing in a SELECT query, below. This doesn't look like a valid query to me. (Note that SQL_CALC_ROWS is omitted by design, I hacked it out as the site doesn't need pagination. This was long after the problem, so it's unrelated.)
SELECT _synfresh FROM wp_9_posts LEFT JOIN wp_9_postmeta ON [...]
Additionally, I'm getting a shedload of errors in the error log, that seem to be generated by an errant query in FWP that's trying to JOIN the same table to itself.
[Wed Aug 21 00:01:17 2013] [error] [client 127.0.0.1] WordPress database error Not unique table/alias: 'wp_12_postmeta' for query SELECT wp_12_posts.ID, wp_12_posts.guid, wp_12_posts.post_title, wp_12_postmeta.meta_value FROM wp_12_posts INNER JOIN wp_12_postmeta ON (wp_12_posts.ID = wp_12_postmeta.post_id)LEFT JOIN wp_12_postmeta ON wp_12_posts.ID = wp_12_postmeta.post_id AND wp_12_postmeta.meta_key = 'fnp_featured_article' AND wp_12_postmeta.meta_value >= '1376780477' WHERE 1=1 AND (wp_12_postmeta.meta_key = '_feedwordpress_retire_me_15' AND wp_12_postmeta.meta_value = '1') AND (wp_12_posts.post_status <> 'fwpretired') GROUP BY wp_12_posts.ID ORDER BY wp_12_postmeta.meta_key DESC, wp_12_posts.post_modified DESC LIMIT 0, 10 made by require('wp-blog-header.php'), require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, FeedWordPress->init, FeedWordPress->update_magic_url, FeedWordPress->update, do_action('feedwordpress_update_complete'), call_user_func_array, SyndicatedLink->process_retirements, WP_Query->__construct, WP_Query->query, WP_Query->get_posts
/me crossed fingers someone from FWP hangs out here!