How can I start a program from a login batch script if the Command Prompt is disabled?

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http://serverfault.com – Our Terminal Servers has two Group Policies in place: one that includes disabling the command prompt, and another that runs a batch script to startup a program upon login. But the startup program never gets launched. I've tried running it manually and am getting an error that "The command prompt has been disabled by your administrator", so I am guessing the command prompt restriction is getting applied before the login script gets run, but I'm not sure what I can do about this. (The program starts up fine if I login with a user that doesn't have the command prompt restriction) Is there a way (HowTos)