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All this trouble seems related to the sound-device configuration and the respective ALSA driver (module). And you did not tell which one it is about :) There's not much I can do to help you at the moment, as the issue seems to be unrelated to JACK (or QjackCtl for that matter).

Please, I''ll recommend you try first with alsamixer whether you can set the device channels as your desires, if possible at all. Or you could go to the ALSA forums or mail-list and ask for some insider help. I'm afraid I can't really tell you anything more in concrete, on how or what, sorry.

Cheers