I have been fighting performance problems on a fairly large installation which I have narrowed down to the stats generation query "INSERT INTO mdl_stats_daily (stattype, timeend, courseid, roleid, stat1, stat2) SELECT 'enrolments', timeend, courseid, roleid, COUNT(DISTINCT...." that is run by the stats generation routines. According to the admin UI, it should be running at 2AM, but I am finding it running in the early evenings (6-8PM) during out peak usage times and it brings the system grinding to a halt. If I kill the query, performance returns to normal. I don't know yet if it's not honoring the schedule at all and is running everytime the cron job runs, or if it's just offset incorrectly. As I discover more I will update this report.
For the time being, I've disabled statistics gathering on this system in the hopes that it will stop running and the system will remain usable. We'll see if that is the case tonight.
A discussion on this has been opened in the forums here: http://moodle.org/mod/forum/post.php?reply=458555