Based on you being able to change the root password with a sys admin account, eludes to the root user being deactivated on your system. The root user doesn't have to be live for you to be able to login with it.
You can confirm this if you login with the root user and correct password and get a message saying something like "Root User account is disabled in this system".
In which case, you need to do this:
On the VM, log into the terminal as root (like what you did in the manuals) and go to the matrix home directory (I think it is located at /var/www/matrix). Then load up main.inc in an editor (eg. vim data/private/conf/main.inc or nano data/private/conf/main.inc) and change SQ_CONF_ROOT_USER_DISABLED from 1 to 0. This should enable the root user again. For more information, read: http://manuals.matri...c#user-settings
See thread: http://forums.squizsuite.net/index.php?showtopic=12506
Does that help?