I manage a moderately large site (80 000 pages view and 150 000 actions daily). When creating a custom segment based on a custom variable value, piwik seems to try to suggest a list of value extracted from the database. Unfortunately, one of the sql requests used for this takes more than 10 minutes to accomplish (actually, I never let it finish since i'm always running out of patience) and literally clog my mysql server which completely freeze:

 SELECT sub.* FROM ( SELECT log_inner.* FROM ( SELECT log_visit.* FROM piwik_log_visit AS log_visit LEFT JOIN piwik_log_link_visit_action AS log_link_visit_action ON log_link_visit_action.idvisit = log_visit.idvisit WHERE ( log_visit.idsite in ('9') AND log_visit.visit_last_action_time >= '2014-12-24 23:00:00' ) AND ( ( log_link_visit_action.custom_var_v3 IS NOT NULL AND (log_link_visit_action.custom_var_v3 <> '' OR log_link_visit_action.custom_var_v3 = 0) ) ) GROUP BY log_visit.idvisit ) AS log_inner ORDER BY idsite, visit_last_action_time DESC LIMIT 0, 400 ) AS sub GROUP BY sub.idvisit ORDER BY sub.visit_last_action_time DESC

Live reports are disabled (by browser_archiving_disabled_enforce=1) in my config file and new segments are always set to be pre-processed (and i have a crontab which trigger core:achive every hour). Knowing my site might be larger than the average, I do everything to tune piwik by pre-processing as much as I can and then this "not so useful" feature I can't disable ruins it all...