Read a few bug reports (going back to 2009!) around where users couldn't use their microphone with HDA Intel/ALC269. I had one set up JACK for 2 playback channels and 1 capture channel, make an .asoundrc to route everything to pulse which is started with a configuration only using module-jack-sink and module-jack-source, start it up and the microphone and the whole setup worked. But that's quite a hassle for a workaround!
I had suspicions that it was the stereo mic causing problem and forcing mono would work and it seems to be the case. I attached a patch, hoping that the fix might be as simple as forcing mono at the ALSA level, but I don't think it'll be that simple... Can someone more experienced see if more is needed, and if not then commit it?
(orig file is from 3.0-rc1 source)