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well, I mean that if I open the Patchbay window once qjackctl has started, another patch is selected from the drop down menu AND the "Activate" button is not pressed. I would like qjackctl to start and "select" the patch I give it on the command line and "press" the Activate button. Is this what the -a switch is supposed to do or have I misunderstood?

I looked at that "Active patchbay persistence", it was unchecked. I checked it (it wasn't first) and selected one of my patchbays from the drop down menu. Now, when I start qjackctl with the command I gave in my first post, the patchbay still doesn't get "activated" as I'd like it to, but in Setup\Options\Connections\Active patchbay persistence the patchbay in the text field is now the one I passed to the -a switch on the command line.