ciao,

rispondo alle tue domande. Il sistema è:
Linux version 3.2.0-40-generic (buildd@allspice) (gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) ) #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013

la rete funziona, si tratta di un server remoto (no hosting)

pacchetti installati:
ii libdbd-mysql-perl 4.020-1build2 Perl5 database interface to the MySQL database
ii libmysqlclient18 5.5.31-0ubuntu0.12.04.1 MySQL database client library
ii mysql-client 5.5.31-0ubuntu0.12.04.1 MySQL database client (metapackage depending on the latest version)
ii mysql-client-5.5 5.5.31-0ubuntu0.12.04.1 MySQL database client binaries
ii mysql-client-core-5.5 5.5.29-0ubuntu0.12.04.2 MySQL database core client binaries
ii mysql-common 5.5.31-0ubuntu0.12.04.1 MySQL database common files, e.g. /etc/mysql/my.cnf
rc mysql-navigator 1.4.2-14 GUI client program for MySQL database server
ii mysql-server 5.5.31-0ubuntu0.12.04.1 MySQL database server (metapackage depending on the latest version)
ii mysql-server-5.5 5.5.31-0ubuntu0.12.04.1 MySQL database server binaries and system database setup
ii mysql-server-core-5.5 5.5.31-0ubuntu0.12.04.1 MySQL database server binaries
ii mysql-workbench-data 5.2.38+dfsg-3 MySQL Workbench -- architecture independent data
ii php5-mysql 5.3.10-1ubuntu3.6 MySQL module for php5
ii python-mysql.connector 0.3.2-1 pure Python implementation of MySQL Client/Server protocol

se gira

1000 6134 0.0 0.0 149672 6712 pts/4 T May11 0:00 gksudo vi /etc/mysql/my.cnf
root 6135 0.0 0.0 62192 1936 ? Ss May11 0:00 /usr/bin/sudo -H -S -p GNOME_SUDO_PASS -u root -- vi /etc/mysql/my.cnf
root 6136 0.0 0.0 27204 1684 ? S May11 0:00 vi /etc/mysql/my.cnf
1000 6148 0.0 0.0 149672 6716 pts/4 T May11 0:00 gksudo vi /etc/mysql/my.cnf
root 6149 0.0 0.0 62192 1936 ? Ss May11 0:00 /usr/bin/sudo -H -S -p GNOME_SUDO_PASS -u root -- vi /etc/mysql/my.cnf
root 6150 0.0 0.0 27144 1788 ? S May11 0:00 vi /etc/mysql/my.cnf
1000 18518 0.0 0.0 13640 912 pts/7 S+ 22:22 0:00 grep --color=auto mysql
1000 28567 0.0 0.0 16552 1380 ? S May07 0:00 /bin/bash /usr/lib/mysql-workbench/bin/mysql-workbench
1000 28569 0.0 0.0 4400 616 ? S May07 0:00 /bin/sh /usr/bin/catchsegv /usr/lib/mysql-workbench/bin/mysql-workbench-bin
1000 28571 0.0 0.1 456484 61384 ? SL May07 1:53 /usr/lib/mysql-workbench/bin/mysql-workbench-bin
cataldo 30763 0.3 0.0 10170984 0 ? Sl Apr26 113:52 /usr/lib/jvm/default-java/bin/java -Dfile.encoding=UTF-8 -classpath /home/cataldo/NetBeansProjects/eVSM/lib/derbyclient.jar:/home/cataldo/NetBeansProjects/eVSM/lib/log4j-1.2.15.jar:/home/cataldo/NetBeansProjects/eVSM/lib/lucene-core-3.0.3.jar:/home/cataldo/NetBeansProjects/eVSM/lib/lucene-demos-3.0.3.jar:/home/cataldo/NetBeansProjects/eVSM/lib/mysql-connector-java-5.1.13-bin.jar:/home/cataldo/NetBeansProjects/eVSM/build/classes it.uniba.di.swap.eVSM.context.experiment.Main

si è aggiunto un nuovo problema: non riesco ad accedere da phphmyadmin come utente root e se provo a farlo da riga di comando ricevo l'errore:

mysql -u root -p
Enter password:
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

è un vero casino..spero mi potete aiutare ad uscirne.
grazie.
ciao