On a Windows 2008 R2 server with the Remote Desktop Services role installed, I have used a local group policy to start a program automatically. How do I log into the console session to manage the server using Remote Desktop in this scenario? In other words, how do I log in to manage the server without having the program start? The /admin switch doesn't work. It did when connecting to Windows 2003 Terminal Service servers.
Starting the program with Local Group Policy isn't, probably, the best way to do what you're looking for.
In Terminal Services environments generally one uses Loopback Group Policy processing (in either Merge or Replace mode) to apply a set of user policy settings to users logging-on to the Terminal Server computer. For "Administrators", typically one would "Deny" the "Apply Group Policy" right to the GPO containing the settings that aren't appropriate for "Administrator" users (like starting a program automatically on logon).
The Multiple Local Group Policy object (MLGPO) functionality can accomodate what you want, as well, but I discourage people from using it in Domain environments. Generally it's better to put your GPOs in the Directory because, in the future, you may have a different (or multiple) server computers in the Terminal Server role. Using GPOs in the Directory means that you need only put new Terminal Server computers into the correct OU to have them "do the right thing", as opposed to having to manually replicate MLGPO settings "by hand" between machines. (In general, you should only want to do a given thing once...)
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Sorry it took so long to understand, but when you see it, you just soak in all the details, but to me, it was just not coming across.
Yes, now that I had enough information to even understand the problem, I was getting to that. I would make it a user policy, and just move the users, administrator for example, to a different OU, so it is not affected by the policy that starts the program. If you already create a separate OU for your users (I highly recommend this anyway), at least administrator in the default users OU won't have to be touched. Any other users you want to exempt, you should move out too.
I will keep the rest of the answer for reference.
2008 Server no longer supports connecting to the console:
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Which version of RDP uses the client you are connecting from? Try to use the /console switch.