@Mitcho: I'm not sure this is related, but I'm getting YARPP-related errors in my PHP error log when running YARPP and W3 Total Cache (W3TC). I have experienced this with W3 Total Cache database caching "enabled" but I seem to get a greater volume of errors when W3TC database caching is "disabled".
Here are a couple of typical example entries (this happens with other post IDs).
[15-Aug-2011 07:27:22] WordPress database error MySQL server has gone away for query select count(*) as count from wp_yarpp_related_cache where reference_ID = 8511 made by require, require_once, include, related_posts, yarpp_related, yarpp_cache_enforce, YARPP_Cache_Tables->is_cached, W3_Db->query
[15-Aug-2011 07:27:22] WordPress database error MySQL server has gone away for query SELECT wp_posts.* FROM wp_posts WHERE 1=1 AND wp_posts.ID = 8511 AND wp_posts.post_type = 'post' AND (wp_posts.post_status = 'publish') ORDER BY wp_posts.post_date DESC made by require, require_once, include, related_posts, yarpp_related, yarpp_cache_enforce, YARPP_Cache_Tables->cache_keywords, post_body_keywords, get_posts, WP_Query->query, WP_Query->get_posts, W3_Db->query
[15-Aug-2011 07:27:22] WordPress database error MySQL server has gone away for query select body from wp_yarpp_keyword_cache where ID = 8511 made by require, require_once, include, related_posts, yarpp_related, yarpp_cache_enforce, YARPP_Cache_Tables->update, yarpp_sql, YARPP_Cache_Tables->get_keywords, W3_Db->query
[15-Aug-2011 07:27:22] WordPress database error MySQL server has gone away for query select title from wp_yarpp_keyword_cache where ID = 8511 made by require, require_once, include, related_posts, yarpp_related, yarpp_cache_enforce, YARPP_Cache_Tables->update, yarpp_sql, YARPP_Cache_Tables->get_keywords, W3_Db->query
Would emptying the YARPP cache table help?
Is there a W3TC setup or cache and table emptying best practice that users of YARPP and caching plugins should employ?
My Setup:
Wordpress 3.0.4
YARPP: 3.3.2
W3 Total Cache: 0.9.2.3
Host: Hostgator