My ArcGIS Server site was created successfully and arcgis server was up and running. At a later date some network IT policies were run on the system after which my ArcGIS Server services were all in the stopping mode (hung forever). When I checked my logs I found the following error:
"Failed to apply cluster protocol to cluster 'default'. C:\Program Files\ArcGIS\Server\geronimo\var\config\config-substitutions.properties (Access is denied) "
As muhannad S. pointed out I just checked the arcgis account under Users and Groups and found it be a member of just the Users group. Adding it back to the Administrators group resolved the issue.