It is either an issue with your file system or with your mysql database.
On some webhosting configurations, WordPress automatic updates fail. In my experience, if it is not file permission, then it is an issue related to file ownership. Try the FTP method. Add the following lines in your wp-config.php
define('FS_METHOD', 'ftpext');
define('FTP_USER', 'YOUR FTP LOGIN');
define('FTP_PASS', 'YOUR FTP PASSWORD');
define('FTP_HOST', 'YOUR FTP HOST (without http:// or ftp://)');
define('FTP_SSL', false);
If still a no-go, see: http://codex.wordpress.org/Editing_wp-config.php#Override_of_default_file_permissions for alternative methods.