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.matrix.squizsuite.net/server-administrator/chapters/annotated-main.inc#user-settings
That's weird, that setting is not on by default, and was not on when I tested the evaluation VM. If anyone else gets this issue as well after setting up and installing the VM, please post here.