I recently did a clean install and ran into (what I believe to be) the same problem. I believe that during the upgrade, my user was not added to the mythtv group. I'm not an expert by any means, but my understanding is that my username needs to be in that group. I did attempt to run mythtv-setup as -u mythtv, but it didn't work.
What fixed the problem for me was:
Follow the section for starting mythtv-setup (below) and add your user to the mythtv group. Logout and then login again. Then run mythtv-setup again under your username.
mythtv-setup must either be launched as a user that is in the mythtv group.
Next, add yourself and any other users that need MythTV acces to the mythtv group.
To add users to the mythtv group, use this command:
# sudo usermod -a -G mythtv USERNAME
Where USERNAME is the name of the user you are adding to the mythtv group.
VERY IMPORTANT: If you do not add your main user account to the mythtv group, you will get the dreaded database errors when you run mythtv-setup! For the addition to the group to take effect, a fresh login needs to occur-- so log out of your current session and then log back in right now.
Once your are in the mythtv group and have logged out/in, you will be able to launch mythtv-setup.