Thanks to Jon's Blog on 04/18/2006 I was able to follow his instructions and add Atlas/Ajax to my DNN 4.3.1.  Everything worked perfect and I was so happy with the site, especially when I added the UpdateProgress control.  As I said all the modules - Including custom modules - worked fine except for two modules, which both included:

 <Script langauge="Javascript">... ... ... ...</script>

The problem with both modules is that they acted as if there was no java script within the html code.  As a matter of fact I viewed the source of the resulted web page and sure enough there was no Java script.  Knowing that both modules worked fine and are working fine when I remove the atlas controls, I thought it is a bug with Atlas.  However, when I created a completely separate Atlas project - not DNN - and I used a simple aspx & ascx code, it worked fine.  Has any one experienced the same thing?  I understand that Atlas is not supported by DNN yet, But the site looks so great now that I hate to stop adding Atlas controls just because of this reason.  Any help is appreciated.