Most likely the program was open while running the command line. The program must be closed in order to run from the command line. Also, for deployment, the program needs to be configured for the user under whom the command line is run. Don't let a system account run the job because the program has no settings for that user. 

Every time a user is working with the command line, all actions are logged. Any issue encountered by the program can be found there. Go to the menu item Log --> Daily log and look up what happened.