I have the same problem and it drives me nuts. Sitemapper finds only the index page in site www.kerolamps.com; I reviewed all and nothing I have done made a difference. It has a similar DHTML menu as my other site www.visitmajorscreek.com which it crawls without problems. Please help to restore my sanity!
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.