Terminal Services Auto Loading Programs

We use Terminal Services only for remote administration of our server. We seem to be running into a problems with the server automatically loading programs when we log in through Terminal Services. Normally it is programs that are actually alreadyrunning on ther server, then Terminal Services starts them again and we get an error because the programs isn’t meant to be running twice. Is there a way to prevent certain things from launching when we use Terminal Services? When we log in we useAdministrator so we can get all of our screen settings and things the same. Any help is appreciated!