I want to run pulseaudio from startup to deal with system sounds etc and be able to run jack from qjackctl for use with audio applications (LMMS, ardour, rosegarden etc) I'm having issues when i start up, the sound applet does not allow me to control the volume. When I click sound preferences it says "waiting for sound system to respond" yet the sound still plays in rhythmbox etc.
This might not be the correct answer, but I'd recommend bringing up JACK only when you need it. Otherwise, things can get crazy with sound.
for some reason pavucontrol had been uninstalled. just had to reinstall it.