Yeah, I agree with bobby, the password prompt is a little misleading. I belive you can continue without any dire consequences.
It looks like the .saveconfig had the wrong mysql password:
The only reason I say that is I had the exact same problem.
Sat Apr 15 12:41:22 2006: Stopping zimbra services
Sat Apr 15 12:41:32 2006: Checking mysql status
Sat Apr 15 12:41:33 2006: Starting mysql
Sat Apr 15 12:41:35 2006: SELECT value FROM config WHERE name = 'db.version'
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/opt/zimbra/db/mysql.sock' (2)
Error while running '/opt/zimbra/bin/mysql --user=zimbra --password=ytFv6o.zuByfvyAWfeUZCaV.eZEAL --database=zimbra --batch --skip-column-names'. at /opt/zimbra/libexec/scripts/Migrate.pm line 134.
Do you know your sql password? If not, you're going to have to run --skip-grant-tables on mysql and change the password (both root and zimbra). If you'd like detailed instructions, do a search on changing the mysql password.
zmlocalconfig -e -f mysql_root_password='password_here';
zmlocalconfig -e -f zimbra_mysql_password='password_here';
Then stop mysql with the skip-grant-tables and start it normally. You can test to make sure that things are working by:
If it lets you in, then you're okay.
If you get in, run /opt/zimbra/libexec/zmsetup.pl and continue.