The key word that are listed in your site stats and in the google stats are only the key words that users entered in their search to find your site, this does not mean that google only has those key works on file for your site, it only the words used by users to find your site.
Google now uses all contents of a sites page as keywords, and does not really matter what key words you place in the meta tag section
But to allow any search engine including google to index all pages of your site to gather key words then in the meta tag section you have to give the search engines the permission to index all pages using this meta line:
<meta name="googlebot" content="index, follow">
By default this line use to be setup like this and did not allow the indexing of all pages:
<meta name="googlebot" content="noindex, nofollow">