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Here is the exact issue:

I have a client app calling a wcf service, in both the client app and the wcf service i have set the time outs to be over 3 hrs. when the service runs about 20 min there is no issue but more than than it times out in a weird way. I started debugging the service to see what actually happens since the time outs shouldn't be an issue. I noticed that the wcf service does not time out if it takes an hour to run. It runs to completion, also on the client side it waits for the response for that whole time with out timing out. When the service goes through IIS to send the response back to the client, IIS or something decides somehow that the response time has passed and sends a Time out to the client. I have checked the Application pool and I have set it to not restart for many hours and i changed the idle time to be more than an hour. Does anyone know what the cause is?

Thanks, Marios