It shouldnt matter how many times you run update, it should run through the whole update again.
The missing backup module in the menu sounds to me like the backup module has not updated on your system. If you are comfortable with SSH you can check its status with the following commands:
cd /home/pi/backup
git status
you could then try updating it with:
git pull
if you have a local change it may not update and that may be our problem, could you let me know what you see?
Another option to try is to run a full update manually you can do this with the manual update steps described at the bottom of the page here: https://community.openenergymonitor.org/t/upgrading-emonsd-07nov16-to-latest-via-emonpi-emonbase-update/11051