Thank you for replying - unfortunately I had to delete the instance and start over due to time restraints but I will answer your questions in case it can shed some light on what happened.
I was prompted for a password after calling sudo emacs on the bitnami.conf. I was about to configure the names of the ssl certs. This surprised me until then I was not asked for a password with sudo emacs, sudo /opt/bitnami/ctlscript.sh restart apache, or sudo apt-get install and similar commands. I had logged out of my instance to requests ssl certs from our provider and when I ssh'd back into AWS I found sudo was requesting a password.
I searched around in case I had previously been given a root password and I found this link:
in which mention it mentions bitnami_credentials and bitnami_appilcation_password was also in the same directory. Both contain the same randomly generated password. Unfortunately sudo emacs (etc) did not accept this password and this lead me to my original post as I had not manually tried to set a password.