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qjackctl configuration is stored and read from ~/.config/rncbc.org/QjackCtl.conf file.

if you have pulseaudio going up (or down) whenever you get jack server running (and what not), then you're probably having it under jackdbus control and then probably never what you may find on ~/.jackdrc will have any sense to reality, which, as a matter of fact, is a write-only file, as far as qjackctl is concerned--iow. qjackctl do NOT read that file whatsoever, it only writes to it (upon user option).

so you probably have been deceived by the jack2 d-bus interface all this time, i suspect, and for that matter, although it may work as one last resort, qjackctl and its author--me, who sticks to jack1 and its command line interface since ever--have no expertise on the whole things that goes under that "marvelous" co-operation that is being done between jack2 and pulseaudio. in fact, as far as jackdbus goes, qjackctl is strictly an one-way interface, that meaning that it only does command it! it doesn't quite control at all what it goes after once the order is spitted out ;)

hth.
cheers