In my continuing effort to help others with needs like mine, I needed to do a quick update to let everyone know that I forgot a step in transitioning to Java 7, making sure my browser plugins were up to date.
For Firefox, in is just a matter of deleting the previous sym-link in the plugins directory (/usr/lib/mozilla/plugins/) and making a new link to the <jre>/lib/<platform>/libnpjp2.so file.
<plaform> is your architecture (in my case amd64).
For Chromium, I just needed to go into the plugins manager inside the browser and disable the old version plugin and the new one was already also installed. Very nice.
At this point, the system is working well and reporting the correct Java version in all places, eg inside the browser and the terminal and the Java programs are running fine. Again, for those of you playing the home game -- My method for getting to Java 7 goes around the mechanism (update-alternatives) and so it may not be the best solution... I welcome doing this the right way as everything on my system is a sym-link and so it is fully reversible if need be. (Other than I deleted the actual executables for Java 6).