SI updates your custom.config.php file if it is missing tags that have been added to config.php. To do this, it renames your custom.config.php file to custom.config.php.old and then creates a new custom.config.php and loads the data in it. If the application does not have write access to the config directory, it cannot do this.
You need to make sure the application has write access to this directory. Also to the public and tmp directories.