Im having a similar problem... I uninstalled the w3tc cache from a multisite which i was having problems with and i still see on logs errors like the following:
[25-Jul-2012 18:21:16] Error Duplicate entry 'ptthemes_content_excerpt_readmore' for key 'item_id' de la base de datos de WordPress para la consulta INSERT INTOwp_67_option_tree(item_id,item_title,item_desc,item_type,item_options) VALUES ('ptthemes_content_excerpt_readmore','Content Excerpt \"Read More\" Link Text','Enter Content Excerpt \"Read More\" Link Text','input','') realizada por require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('after_setup_theme'), call_user_func_array, after_setup_theme_option_tree_setup, W3_Db->insert, W3_Db_Nocache->query, W3_Db->query_nocache
I cleared all database cache when i disabled the plugin. How can i fix this? Shall i install the plugin again and try to clear cache some other way?