You are getting this error because you may be running the ASP.NET 1.1 and ASP.NET 2.0 in the same process pool. In IIS you cannot run both version of .NET in the same process and this will cause the error.

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. This can cause sporadic behaviour if you are using the server at the same time as another developer and you have applications using different versions of the framework in the same application pool.

To fix this issue make sure you have created a new application pool one for ASP.NET 1.1 and one for ASP.NET 2.0

How to Create New Application Pool in IIS

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