OK, so I used hdajackretask to set jack detection to 'not present' for
the front and back mic inputs, and things work as expected (I can select
them from the 'sound settings' gui)

So is this just my sound card claiming that the front mic has jack sense
when it doesn't, or is there a bug in the alsa driver?

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https://bugs.launchpad.net/bugs/1275178

Title:
  [GA-MA780G-UD3H, Realtek ALC889A, Pink Mic, Front] Recording problem

Status in “pulseaudio” package in Ubuntu:
  Incomplete

Bug description:
  Pulseaudio doesn't detect the analogue input.  The input tab of the
  sound settings only shows digital input (s/pdif).  So through alsa,
  recording works (if a little quiet), but through pulse it doesn't.

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: alsa-base 1.0.25+dfsg-0ubuntu4
  ProcVersionSignature: Ubuntu 3.13.0-6.23-generic 3.13.0
  Uname: Linux 3.13.0-6-generic x86_64
  ApportVersion: 2.13.2-0ubuntu2
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  michaelb   2064 F.... pulseaudio
   /dev/snd/controlC0:  michaelb   2064 F.... pulseaudio
  CurrentDesktop: Unity
  Date: Sat Feb  1 14:34:50 2014
  InstallationDate: Installed on 2013-06-22 (224 days ago)
  InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Alpha amd64 (20130621)
  PackageArchitecture: all
  SourcePackage: alsa-driver
  Symptom: audio
  Symptom_AlsaRecordingTest: ALSA recording test through plughw:SB successful
  Symptom_Card: Built-in Audio - HDA ATI SB
  Symptom_Jack: Pink Mic, Front
  Symptom_PulseAudioRecordingTest: PulseAudio recording test through plughw:SB 
failed
  Symptom_Type: Only some of inputs are working
  Title: [GA-MA780G-UD3H, Realtek ALC889A, Pink Mic, Front] Recording problem
  UpgradeStatus: Upgraded to trusty on 2013-12-05 (57 days ago)
  dmi.bios.date: 07/13/2010
  dmi.bios.vendor: Award Software International, Inc.
  dmi.bios.version: F6b
  dmi.board.name: GA-MA780G-UD3H
  dmi.board.vendor: Gigabyte Technology Co., Ltd.
  dmi.board.version: x.x
  dmi.chassis.type: 3
  dmi.chassis.vendor: Gigabyte Technology Co., Ltd.
  dmi.modalias: 
dmi:bvnAwardSoftwareInternational,Inc.:bvrF6b:bd07/13/2010:svnGigabyteTechnologyCo.,Ltd.:pnGA-MA780G-UD3H:pvr:rvnGigabyteTechnologyCo.,Ltd.:rnGA-MA780G-UD3H:rvrx.x:cvnGigabyteTechnologyCo.,Ltd.:ct3:cvr:
  dmi.product.name: GA-MA780G-UD3H
  dmi.sys.vendor: Gigabyte Technology Co., Ltd.

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