After I use Jack, the PulseAudio outputs and inputs are replaced by a dummy device. I've tried to kill PulseAudio and reload Alsa, but the only way I can use an Alsa-based application again is to reboot. I know that there must be a way to fix the problem without rebooting. I have had this problem in multiple Linux distros, including Ubuntu and currently Fedora 19.
service alsa-utils restart:
Redirecting to /bin/systemctl restart alsa-utils.service Failed to issue method call: Unit alsa-utils.service failed to load: No such file or directory. See system logs and 'systemctl status alsa-utils.service' for details.
systemctl status alsa-utils.service:
alsa-utils.service Loaded: error (Reason: No such file or directory) Active: inactive (dead)
alsactl kill quit and
alsactl init proceed with no errors.