If your .htaccess is not writeable (unix rights 777) then wordpress can not auto-update that file. Either set it to those rights OR manually update it. Not sure about older releases of WP, but WP2 gives you the code to copy and paste into your .htaccess
Have you tried the new akismet available with WP2? You will have to get an API key from wordpress (see your account or the original email you recieved for the key)
