I found this on the MySQL Dev site which I think may be the problem?

"You can also get these errors if you send a query to the server that is incorrect or too large. If mysql receives a packet that is too large or out of order, it assumes that something has gone wrong with the client and closes the connection. If you need big queries (for example, if you are working with big BLOB columns), you can increase the query limit by setting the server's max_allowed_packet variable, which has a default value of 1MB. You may also need to increase the maximum packet size on the client end. More information on setting the packet size is given in Section B.1.2.9, “Packet too large”."