The search engines see a link like http://mysite.com/ as a different page than http://mysite.com/index.php or http://www.mysite.com. Since all three links will point to the same page, they may perceive this as an attempt to fool them. They call this "Duplicate Content" and may ban a page, or even a site, for it. You can tell if your site is using both links by clicking in your logo. Doing that in a standard oscommerce shop will cause the url to change so that it contains index.php. This change will alter the code so that only one of the links will be a direct link. The others will be redirected to that main link, thus preventing the possibility of a duplicate content situation.