Problem with # use in CSS of Joomla template and HTML

I'm using a Joomla Art template ona  site Im working on. I recently launched the site. After a week of not being indexed and not being indexed in Google Webmaster Tools, I dug a little deeper.

I ran the site through:

http://validator.w3.org/checklink

To check for any dead links or link errors.

The main error found was

Lines: 70, 97, 156 http://mysite.com/
    Status: 200 OK

    Some of the links to this resource point to broken URI fragments (such as index.html#fragment).
    Broken fragments:

        * http://mysite.com/#ja-col2 (line 70)


Now what's happening is that the Joomla Art template I'm using has defined various elements in the CSS such as #ja-col and #ja-mainnav. ja-col is used in menu items that then link to articles.

Now the problem is this. In the HTMl, they're saying <a href=#jacol-2..... but this is referencing a style where as it should be referencing a content link. The site works fine and can be browsed without problems. However, Googlebot and other crawlers cant access the other content.

I have absolutely no idea how to resolve this issue. Any help/ideas would be much appreciated.

Thanks.

O2K