Oh, thanks! Your comment made me look again and now I've figured it out! I had "Secure Keyboard Entry" turned on in Terminal.app. Apparently this prevents the

Oh, thanks! Your comment made me look again and now I've figured it out! I had "Secure Keyboard Entry" turned on in Terminal.app. Apparently this prevents the authentication pop-up (or anything else, presumably) from taking focus away from Terminal. Turning it off solves the focus issue!