Back in November, I filed MySQL bug 67448, talking about a different type of max_allowed_packet problem.
See, an application had put data into the database, but could not retrieve it without getting max_allowed_packet. With the help of some really smart community folks (named Jesper Hansen, Brandon Johnson and Shane Bester), we determined that MySQL actually has 2 different max_allowed_packet settings: client and server.
When you change the max_allowed_packet variable, you are changing the server variable if it is in [mysqld] and the client variable if it is in [client] or [mysql] or whatever client you have. As far as we can tell, theres no way to actually view what the client variable is, as looking at both the session and global max_allowed_packet variable shows you the server variable.
If max_allowed_packet is not set by the client, it defaults to 16M. The proposed solution is to allow it to be increased for non-interactive clients, and the bug has been verified as a feature request, though it has not been implemented yet.