This kinda reminds me of what happens when I run a script from udev. the
rule is for a usb audio device. the script runs an amixer command to set
device name and volume level, then runs jack. if I then run qjackctl
manually it doesn't 'see' jack running. a quick look in qps showed that
jackd is running as root. been banging my head against the wall trying to
figure out how to run the script as my_user instead of root. not sure if
this is in the neighborhood of what you're experiencing.
/usr/bin/jackd -dalsa -d hw:3 -r44100 -p1024 -n2
amixer -c 3 -- sset Speaker 10%
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