Mandeep,
Robert
1. IIS is running fine.
2. There is one more application where we see all our map services "arcgis" and it is working fine.
3. I tested with Web.config file too but it didn't make any difference. I have kept it now in Proxy folder.
Services hosted on other webapp named arcgis can be seen in http://arcgis01.madisoncty.com/arcgis/rest/services
But I did notice one thing that arcgis application is assigned to ArcGISWebAdaptorAppPool and this adapter is attached to .net v2.0 in Application pools as we have both v2.0 and v4.0 for .net. Does this can create any problem.
Thanks
Mandeep