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I really can't give you much help here: but have you tried to redirect the internal mic through PA and then read its input from the PA JACK Sink?

I guess you must do that at least once, otherwise I cannot foresee it working anyhow... but again, I'm not the best source of knowledge re. PA... ;)

OTOH. if you want to put PA out of the picture, you can try to just uninstall the pulseaudio-module-jack package ie. NOT the whole pulseaudio installation, otherwise you'll end with a severely crippled linux desktop sound system and probably you will surely regret that ;)

Note you can always re-install pulseaudio-module-jack back later to get your stuff as it were before this trouble.

You may also have to edit ~/.pulse/client.conf and make it say autospawn = no, but twice again, i'm no expert on this.

And don't EVER touch the "Advance" settings tab on QjackCtl! If you done that already then you're doomed! :) Haven't you read the warning in the top there? Please revert all your changes you possibly have committed in there and hope for the best ;)

Then resort to Options tab > Scripting, and maybe set it like this:

hth.
cheers