MySQL server has gone away - in exactly 60 seconds

The php option mysql.connect_timeout is the reason for this. It's not only used for connect timeout, but as well as waiting for the first answer from the server. You can increase it like this:

ini_set('mysql.connect_timeout', 300);
ini_set('default_socket_timeout', 300); 

When I ran into this problem, it wasn't caused by wait_timeout (which was set to the default 8 hours) but by max_allowed_packet with a large INSERT statement. Changing max_allowed_packet from PHP had no effect, but when I changed it in the mysqld section of /etc/my.cnf and restarted the MySQL server, the problem disappeared.