Hi Howard,
Thanks for your response. Debugging is up to 'developer' and I've looked at the MySQL error logs but there's nothing there. The only place I see the errors logged is in the php error log.
There are a couple of other facts I failed to mention last time:
1. The same phenomenon occurs on our development/test instance. This instance is created from a snapshot of the production instance and is on completely separate hardware (though with the same configuration).
2. We have another strange phenomenon, which is that it takes a very long time to delete a course that has user data. It can take anywhere from a few minutes for a very small course to and hour or two, with multiple timeouts on the deletion, for a larger course. From what I can tell, the timeouts are on session locks, but that too is something of a mystery.
Do either of those provide a clue? There's really nothing special about our setup. All of the servers are Windows 2008 R2. Apache/Moodle are hosted on separate boxes from the databases, but there's no cluster. There may be load-balancing at play - I'm going to check into that.
Thanks,
Trevar