I have my wp-config.php one directory-level up of the root, and now since WordPress 3.7, every time a new update is installed a new wp-config.php is created in it's normal locations but the same database details as my original except the table prefix. This, obviously, causes WordPress not to be able to find any of the tables, and try to make a new install in the database.
For the time being I am forced to move back my wp-config.php from the directory-up-level, to it's default position, hopefully this will stop the updates creating new files.
Any idea how to properly update wordpress with a wp-config.php in an up-level? Is WordPress getting the table prefix from somewhere else?