Depending on the complexity of your site a lot of data ends up being
collected during a profile run. The first problem with this is that the
database table
holding this information might be growing. Please double check the cron
settings of the cleanup task.
By default MySQL comes with max_allowed_packet set to 1 MB. One
profile run could exceed 1 MB. Please check var/system.log for error
messages and increase this setting in our MySQL server settings
(/etc/mysql/myconf). (Also see: http://dev.mysql.com/doc/refman/5.1/en/packet-too-large.html)