I think more information is needed before you decide you have a penalty. How long has your site been listed on Google? For instance, if you just got a new site listed, you may not have gotten a deep search from their spider yet. Google and other SE’s spider your site differently at different times.
Another possiblity is if you have all of the same names in your title tag. If every page has the same name, SE’s will often only show the one page in it’s results thinking the others are duplicate.
And finally, you should really set up a Google sitemap. http://www.google.com/webmasters/sitemaps/login This will make certain the Google knows about all of the pages on your site.