[ZODB-Dev] RelStorage gives MySQL error when rebuilding catalog in Plone/ZMI

[J Z]

Sorry about the terrible format. Please allow me to try it again.

I have a Plone 4.1 site using RelStorage to store the zodb in MySQL 5.5 
server. The site has 700 objects cataloged and the database is less than
300MB  after packing. I won't consider it's a large site. When I tried to 
"update catalog" or "clear & rebuild" the catalog, I got the following error: 

Traceback (innermost last):
    * Module ZPublisher.Publish, line 134, in publish
    * Module Zope2.App.startup, line 301, in commit
    * Module transaction._manager, line 89, in commit
    * Module transaction._transaction, line 329, in commit
    * Module transaction._transaction, line 443, in _commitResources
    * Module ZODB.Connection, line 567, in commit
    * Module ZODB.Connection, line 623, in _commit
    * Module ZODB.Connection, line 682, in _store_objects
    * Module relstorage.storage, line 571, in store
    * Module relstorage.adapters.mover, line 484, in mysql_store_temp
    * Module relstorage.adapters.batch, line 67, in insert_into
    * Module relstorage.adapters.batch, line 74, in flush
    * Module relstorage.adapters.batch, line 110, in _do_inserts
    * Module MySQLdb.cursors, line 174, in execute
    * Module MySQLdb.connections, line 36, in defaulterrorhandler
OperationalError: (2006, 'MySQL server has gone away') 

The mysql was installed with most default settings. The wait_timeout is
28800 according to phpMyAdmin. Can someone give some idea what 
could be wrong and where I should start looking? Thanks!