Remote Desktop User Treated Differently than Local User

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http://serverfault.com – We have some encoding software running on Windows Server 2008 R2 that when a user is logged in locally he is able to operate the software and everything is fine. When he remote desktops to the computer the software is saying we've reached the maximum number of encoders available for this license. Can anyone think of a way to have a remote desktop user treated as the local user? More information: When the local admin or another domain user logs in it says the software is not registered. I believe the licensing is for one user so this makes sense. The server is part of our domain but not a (HowTos)