Applying the smeplus.sh update to SME Server 6.0.1 I noticed that the updated MySQL server does not restarts right as it should.
The first symptom of this behaviour is an error message that unfortunately I did not write down, coded "ERROR 2002" and generated by the /usr/bin/mysql_fix_privilege_tables procedure that says it can't connect to database using /var/lib/mysql/mysql.sock.
Consequently, the phpmyadmin and twiggi installations fail.
I recovered them both stopping and starting mysqld from another virtual console and then issuing by hand the postinstallation scripts, line by line, from the command line.
I do not know if it is the old server that doesn't shut down completely, or the new one that starts with incorrect parameters, but I think it should be worth having a look at it...