If "skip-networking" is in effect, then MySQL is not listening on any network interfaces (local or otherwise). You can check this with the command (as root):
Code:
netstat -lvpnut | grep 3306
If there is no output, then any application trying to connect to MySQL over the network interface will fail. Your choices are to point the application to the appropriate UNIX socket file (probably something like
/var/lib/mysql/mysql.sock) or enable networking in MySQL.
Edit: missed you saying that the client was connecting OK. In that case, try
logging the activity and see what queries are coming in to MySQL.