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It seems as if MySQLdb is restricting the maximum transfer size for SQL statements. I have set the max_allowed_packet to 128M for mysqld. MySQL documentation says that this needs to be done for the client as well.

+1  A: 

You need to put max_allowed_packet into the [client] section of my.cnf on the machine where the client runs. If you want to, you can specify a different file or group in mysqldb.connect.

Martin v. Löwis