The mysql root password is not used for user authentication in the ispconfig interface. ISPConfig connects to mysql with the user "ispconfig" and not root. The root user is only used to create new client databases. Have you changed the password of the ispconfig mysql user too?
I'm pretty sure I may have at some point.
Should I change the ispconfig mysql password using
update user set Password=PASSWORD('mynewpassword') WHERE User='ispconfig';
Do I need to update an ISPConfig file somewhere when I do?