Over the last seven days, GrabPERF has been running in a very unstable state. This appears to be directly related to the use of InnoDB as the DB engine on a few of the larger tables in the database. [InnoDB changeover discussed here]
Today, the system was offline for several hours before I noticed that the DB had failed to restart properly. Apparently the system simply decided that the InnoDB engine had gone away.
All tables have now been switched back to the good old MyISAM and all the headaches that come with that.