UPDATE: Sucuri notes malware:
This is likely a failed update...you will need to use an FTP tool such as Firebug (and not the file manager from GD :-) to manually overwrite the folders wp-admin and wp-includes - do NOT overwrite the wp-content folder, but do make sure an unedited version of the default theme twentyeleven or twentytwelve are in the theme folder - and rename all other theme and plugin folders to old-folder_name. You will now have your files in place correctly.
Just in case, download the .htacess file (in root) and delete the one in your root folder (reset permalinks once back in admin of site). Also verify settings in wp-config.php.
If any of this is unclear, research them at the search box above (or on Google) but make sure the links are from wordpress.org (as you can trust them).