Derek, 
You may have already solved the problem, but if you want to be able to open/close ports (eg. port 3306) then download and install the port opening rpm from my ftp server at:  
ftp://ftp.westernportmedical.com.au  You need this port opened when using a java applet to connect to a mysql database, but I'm not sure if this is your problem here.  
I have found that whenever I upgrade my e-smith server, for some reason my mysql root password gets corrupted, causing an internal server error message on all php pages which need to connect to the mysql database - from memory the error message reads "unable to connect to database at localhost for passwords Yes (or something similar).  
I have therefore had to reset my mysql root password after I update e-smith.  To find out how to do this, do a google search on mysql+root+password+change ... this URL:  
http://mefriss1.swan.ac.uk/htmlhelp/php/page.php/37/apas04.html  ... tells you how to reset the mysql root password: - 
 "If you have set a root password, but forgot what it was, you can set a new password with the following procedure: 
Take down the mysqld server by sending a kill (not kill -9) to the mysqld server. The pid is stored in a .pid file, which is normally in the MySQL database directory: 
shell kill cat /mysql-data-directory/hostname.pid
You must be either the Unix root user or the same user mysqld runs as to do this. 
Restart mysqld with the -skip-grant-tables option. 
Set a new password with the mysqladmin password command: 
shell mysqladmin -u root password 'mynewpassword'
Now you can either stop mysqld and restart it normally, or just load the privilege tables with: 
shell mysqladmin -h hostname flush-privileges
After this, you should be able to connect using the new password. "
HTH.
- John Mac