On the weekend, I upgraded the database engine for GrabPERF to Mysql 5.1 and switched the main data table from MyISAM to InnoDB.
The switch to InnoDB was done because of the locking issues that were occurring during long queries, especially when doing ad-hoc analysis. The row-level (versus table-level) locking of InnoDB has removed most of these issues.
I have been seeing some strange behavior with the new engine. As a result of this, I will be re-starting the database engine twice a day. There should be no degradation, as this is simply a daemon re-start, not a machine re-start.