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

[J Z]

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!