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We are looking at setting up a terminal server at a company we work with.

They require an application installed on the terminal server which puts configuration files in the Program Data location on Windows 2008.

This application needs to be used by 2 sets of users who will require different configuration files stored within the Program Data folder on the same server.

Rather than using 2 servers is there a application which can deal with this?

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Since the OS has only one ProgramData folder, and the application requires data to be saved there, you might not have a choice about using 2 servers. Have you considered running one terminal server on the physical server normally, and installing the second one using VMWare, VirtualBox, etc? –  charnley Mar 24 '11 at 16:23
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You can publish shortcuts to the applications via an RDP server with one shortcut pointing to one server and the other pointing to another. Just set the security on one fo them to go to a group where all users you want to use that one are members and visa versa.

When the users login to the portal to view their published application shortcuts, they will only be able to run the one that is published to them that points to the correct server.

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