If you checked it from link:sitename in google, then you must know that google shows only a limited number of links there. You can get the overall picture of your site in google webmaster tools. This is the url: http://www.google.com/webmasters/tools and register your site and verify it. It will report you much more stats. Anyways, as other have reported Directory submissions are not going to make any strong marks unless exploring some more ways.
All the directory link do not appear in backlink search becouse it need time to get indexed on that backlink by search engine, it's natural no need to worried