Does the data_intermediate_ad_connection table fields tracker_country, tracker_https, tracker_domain, tracker_page, tracker_query, tracker_referer are still been fill in ? I need to track these when a tracker is trigger from the external websites that will have the beacon.
Make sure you are using the InnoDB engine too. Are the connections idle or waiting or locked? Can you share a screen shoot of 'SHOW PROCESSLIST' when the 3,000 connections are there ?