I have the same problem, but I have only one soundcard: Soundblaster
Audigy ZS 2.

When I start qjackctl (without starting jackd yet!) there is no more
sound from applications like totem or system sounds. Totem just stops at
the current position.

When I left-click the speaker Icon in the upper right corner and go to
settings, hardware, I can select a Profile. When I switch that profile
from "Analog Stereo Output" to "IEC958" or the other way, sound works
again. It does not matter what is selected before starting qjackctl, I
simply have to change the setting.

When I start qjackctl and then jackd and initiate suspend to ram (S3),
jackd ist stopped after resuming from standby. qjackctl still runs. I
start jackd and both audio from jackd and pulseadio is working fine.

I see the problem somewhere in qjackctl. At startup it does something to
pulseaudio or the soudcard, even without starting jackd. Maybe it scans
for available outputs/inputs then... ?

-- 
pulse audio stop when qjackctl is launched
https://bugs.launchpad.net/bugs/231601
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