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The jack1/jack2 thing may be part of my confusion.

I've never been able to find clear instructions as to how to determine which is running.

In this case I'm running whatever is installed with UbuntuStudio 16.04.

As for how the pulse source/sink appears when jack is started. If, pulse somehow is listening for jack to start and connects when it does, then why does the pulse source/sink show up when jack is started from qJackctl, but not when the jack is started from the command line with what is written to .jackdrc... Isn't the command line case just doing the same thing qjackctl is doing?