IIS7.5 Application is using web.config in the root directory instead of its own!

Note: I did not setup a virtual directory its a Application!

Here is the structure

Hard drive folders:

-IISRoot
 -Webpage
  Test.aspx
  web.config

 -WebService
  -Bin
  Service.svc
  web.config

IIS is setup the following way:

-WebSite (Mapping against ISSRoot\Webpage)
 -Service ((Application) mapping against IISRoot\WebService)

Now when i try to run the Service.svc i get a error that a httpHandler was not found ("Could not load type 'Jympa.Nu.FileRequestHandler'")...

Now if i look in the web.config in the root there is a line adding this but the web.config in the webservice is not..

So why is IIS开发者_Go百科 using the wrong web.config?

Edit:

If i remove the web.config in the Webpage folder the service works but the webpage stops to work..

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I found a solution i changed the pipeline mode on the application pool to Integrated.