Yes, it makes perfect sense. You changed the mysql root password (which you shouldn't have done for the reasons I previously outlined), and then used the root user and changed password when you set up phpmyadmin (which you needed to do) and your forum (which you shouldn't have done; the forum doesn't need root access).
What you should do is:
1. Reset the mysql root password as described in my HOWTO.
2. Change the phpmyadmin config to use the new mysql root password.
3. Change the phpbb config to use a completely different user and password--there's no need to use root for this application, and if a security vulnerability in phpbb were to allow the config files to be read, using root would compromise that name and password, exposing your whole database rather than just one set of tables.
Now, as far as Navicat, I've never used it and don't know much (read: anything other than what I see in about 30 seconds on their web site) about it, but I don't think the mysql root user allows remote access by default. This could be your problem.