I have the same problem, and haven't found a solution.  I do have a work-around.
1) Specify the integrated sound card as the only card pulse uses in 
/etc/pulse/default.pa by commenting out the following

### Automatically load driver modules depending on the hardware available
.ifexists module-udev-detect.so
load-module module-udev-detect
.else
### Alternatively use the static hardware detection module (for systems that
### lack udev support)
load-module module-detect
.endif

and adding

load-module module-alsa-sink device=hw:0,0
load-module module-alsa-source device=hw:0,0

Note that I have the integrated card forced to be hw:0,0...

2) Start jackd from the command line using the command line generated by
qjackctl (~/.jackdrc).

-- 
pulse audio stop when qjackctl is launched
https://bugs.launchpad.net/bugs/231601
You received this bug notification because you are a member of Ubuntu
Studio, which is a bug assignee.

Status in “pulseaudio” package in Ubuntu: Confirmed

Bug description:
So, 

I own 2 sound cards, the fisrt is an hda-nvidia integrated to the mother board. 
And for audio working purpose, I use on my worksation a RME hdsp multiface II 
sound card with its pci adapter. I edited the /etc/modprobe.d/alsa-base file to 
set the integrated chipset as default, index=0, and the second as index=1.

The problem I have is that when I launch Qjackctl, even without starting jack, 
Pulse Audio stop to send to sound to my mother board sound card. Very annoying 
problem. Is there a way that Pulse Audio always use the same sound card and 
never stop ?

Toine

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