I think what you're saying is that the front page of your site is listed below your subpages? It's not specifically "screwed up," AltaVista just decided that your subpage seemed more important than your front page.
Does the subpage have a lot more text content than the front page? Or does the subpage have more outgoing or incoming links than your front page? There are a lot of factors as to why one page would be considered more important than the main page of the same site, but I never considered it a big problem, as long as my site was listed!
It often happens with root pages David. Root pages usually have a great deal of conflicting text on the page and don't rank all that well. You will almost always have greater success with sub-pages. The nature of the specific content on the subpages will make them rank higher under targeted terms.