The URL for a feature layer should end with a number, for example /MapServer/0 when used with a Map Service or Feature Service. When used with an Image Service, the URL for a feature layer should end in /MapServer.
The URL for dynamic and tiled services should normally end in /MapServer and also contain /rest/.
Justin,
The answer to your issues are addressed in the documentation:
http://help.arcgis.com/en/webapps/flexviewer/help/index.html#/The_Layer_tag/01m30000000p000000/
<layer label="Test" type="dynamic" visible="true" url="http://localhost/ArcGIS/rest/services/MapDocTest/MapServer"/>
Justin,
If you add it this way can you see it?<layer label="Test" type="dynamic" visible="true" url="http://localhost/ArcGIS/rest/services/MapDocTest/MapServer"/>