We have a Server 2008 R2 terminal server with an application on it that is losing it's authentication to our IIS server. Basically you log in to the application and when you begin to work in it, it tells you it has lost it's connection to the server. At that point, you have to close and reopen the program and it will work again for a while until the same issue occurs. What is weird though is that if we open up Internet Explorer on the server and then launch the application, the problem doesn't occur. So there seems to be some sort of Internet Explorer setting that is getting applied that is allowing the authentication to work.
The application in IIS is using Windows Authentication. Has anyone ever ran in to an issue like this before?