My bad, I should enforce the git pull to prevent this kind of problems, now with this you should have a clean upgraded environment:
cd /var/www/minera
sudo git fetch --all
sudo git reset --hard origin/master
sudo ./upgrade_minera.sh
NOTE: every time you update the system running git commands manually
you have to run ./upgrade_minera.sh too, this resets the notification icon while it does every system upgrade needed.
Thanks for feedbacks guys
PS
autotune saved freq seems to be bugged need to investigate