Simply updating the mxd will not update the service.I believe that you have to literally overwrite the service, i.e. republish it.Here is a related discussion:http://forums.arcgis.com/threads/73931-Problem-updating-a-service-created-from-an-.msd
As Anthony mentioned, you'll just have to restart your service after saving the mxd, not trying to re-publish the service with the same name. In addition, you might have to login to the REST Admin if you're not using ArcGIS 10.1 yet (http://yourmapservice/ArcGIS/rest/admin) and clear the cache. See here for more information.
Jamal,You are using 10.1 and I don't believe that you need to clear the cache.
That is my understanding.
If I were you, I'd migrate away from the Web ADF application in favor of the newer platforms:ArcGIS Viewer for FlexArcGIS Viewer for Silverlight
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