Comment 3 for bug 615869

I had a similar issue. Used Update Manager to upgrade a BioLinux6 installation (Ubuntu 10.04 based). Also hung on "Installing new version of config file /etc/init/mysql.conf ..."

/var/log/daemon.log revealed mysql respawning every 30 seconds as above. This had been going on for over an hour before I noticed. I killed the 'start mysql' process, and the upgrade continued. Installed a few more updates, Update Manager now claims that system is up to date.

Can't seem to start mysql as a service, though:
$ sudo start mysql
mysql start/running
$ ps ax | grep sql
 1347 ? S 5:10 /usr/lib/postgresql/8.4/bin/postgres -D /var/lib/postgresql/8.4/main -c config_file=/etc/postgresql/8.4/main/postgresql.conf
21157 pts/2 S+ 0:00 grep --color=auto sql