I have no idea... is he running the GUI version or the console? I know the GUI version can be set to stop processing when the current WU is finished. The console version has an option called '-oneunit' that will cause it to stop work once the current WU has finished.
Beyond that, I'm not sure right now without knowing more about the setup.
He's running the GUI version with the protein icon in the systray. His folding doesn't "pause when done," it just doesn't automatically start working on the new work unit when it is downloaded.