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Thank you! I have been wrestling with this for 4 hours and couldn't figure out that you have to *manually* select two outputs at a time (left and right).
Clearly this is a BUG in qjackctl's feature of "Create patchbay definition as a snapshot of all actual client connections?" Because that should create
whatever you get after doing it manually the way you described. I am flabbergasted that 14 years after this post this bug is still not fixed :/.