Many web sites use flash, java, or images for their top or side menu links. The fancy rollover effects are esthetically enhancing to the web site’s design so its no mystery why they are popular. However, Google needs plain text links to best navigate your web site.
You can keep the attractive menu at the top of your web site but you should link in plain text to all of your pages at the bottom. A good example is at http://www.adviatech.com, Have your search engine optimization company use that as an example. This simple addition may be what is keeping your search engine optimization goals from being accomplished.