Exact same thing happened to one of my clients on August 21 with same config info and install folder was installed. I managed to fix the website, however i am not sure if it is going to happen again. And no there is no other scripts on the server like WP or Joomla, just CMS Made Simple, latest version.
I also had some other problems with 4 other clients which i posted here:
http://forum.cmsmadesimple.org/viewtopi ... =8&t=73343
It has been a crazy week for me, but finally got 4/5 websites up and running again

One is still suspended due to issue i addressed in the other thread, still working on it.