Sitemapper scans your website in the same way as the spiders from popular search engines such as Google & Bing. This means that it does not follow links in JavaScript, DHTML, or Flash files. Here's why: Search engine spiders can only follow HTML.

Let's use Flash as an example. A Flash-based webpage is pretty and interactive when a human looks at it, but when a search engine spider tries to scan it, all it sees is an <embed> tag. It can't go into the Flash animation to find the links, so it skips past the page, and your site doesn't get a good ranking. Simple as that.

So what's the solution? Use HTML for all your links and navigation. If you want your site to rank well in search engine results, to work correctly on all browsers, and to be accessible to people with disabilities, you have to structure your site with semantically valid HTML and add CSS and JavaScript using the principles of progressive enhancement. For more information about this über-important facet of web design, read this fabulous article at A List Apart.