when updating to drupal 7.41 get WCOD- have to reinstall original installation

I installed the 7.x-1.0-rc2 version and configured it some to test it out; installed on GoDaddy in a sub domain. I kept getting large areas of the screen telling me to there was a security upgrade to the core and I needed to install it. When I looked in the reports nothing showed. However, one screen told me that Drupal 7.39 was installed and I needed to upgrade to 7.41. I have some other sites, production ones, and I run 7.41 on those, so I thought: fine, I will just upgrade.

I did via ftp in the traditional, normal fashion. BUT afterwords all I got anywhere was either WSOD or a completely broken page and could only access admin pages sort of but without any theming whatsoever. This disappeared if I tried to go back.

I was not able to recover, and had to delete the site and start from scratch. Why??? Does this mean that one cannot run upgrades on this site? Also where is the theme located? When I look in the theme folder in the site folder, it's empty??

test site here