I know this is a late response, but wanted to throw something up here to check in case others come across this thread in the future. In the Application's properties, make sure "Allow this application to be deployed as part of a task sequence without being deployed." is checked. This being set on the application, as well as "Install whether or not the user is logged on" in the deployment type's properties should be all you need to install an App as part of the TS.