Now, this is specially for ASP.NET 2.0 developers, who host web applications on a shared IIS.
After deployment, if you have ever received an error message for .Net applications only: “Server Application Unavailable”, then this probably the solution that you are looking at.
First, check the event viewer on the server, if you have an access to it.
General error is that ‘It is not possible to run two different versions of ASP.NET in the same IIS process. Please use the IIS Administration tool to run the application in a separate process.
Information: An application pool is a process that responds to web requests under IIS. An application pool does not have a setting for what type of ASP.Net applications will be run in it. Instead, it loads the appropriate libraries when an ASP.Net application is loaded in the process. Because the libraries for ASP.Net 1.1 and ASP.Net 2.0 are similar, but not the same, the application pool cannot respond to requests for both types of applications at the same time.
Second, make sure that your application pool is dedicated to ASP.NET 2.0 and not ASP.NET 1.1
Try switching between ‘Isolated Application Pool’ and ‘Default Application Pool’
I guess, this will definately make it work! For me, it started working 
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