I notice that you used arecord to record those audio samples. Arecord is
part of ALSA. Do you get the same result if you use the parecord command
to record via Pulseaudio?

PulseAudio does use ALSA, but by using arecord, you are effectively
going to ALSA, and then to Pulse, and then back to ALSA, introducing
extra bits in the chain, which could be the problem.

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https://bugs.launchpad.net/bugs/1100232

Title:
  [SBC-FITPC2, Realtek ALC662 rev1, Blue Line In, Rear] Recording has
  crackeling noise

Status in “pulseaudio” package in Ubuntu:
  New

Bug description:
  Please have a look at these two audio recordings:
  https://dl.dropbox.com/u/6520164/test.wav
  https://dl.dropbox.com/u/6520164/test1.wav

  These were recorded via
  $ arecord > test.wav
  $ arecord -r 48000 -f FLOAT_LE > test1.wav

  The signal should be a 50 Hz Sine wave, however specially in the second 
recording you will oberserve this:
  In regular intervalls the signum of the signal is flipped.

  This leads to a crackling noisy recording.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.10
  Package: pulseaudio 1:2.1-0ubuntu4
  ProcVersionSignature: Ubuntu 3.5.0-21.32-generic 3.5.7.1
  Uname: Linux 3.5.0-21-generic i686
  ApportVersion: 2.6.1-0ubuntu9
  Architecture: i386
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  sb         3534 F.... pulseaudio
  Date: Wed Jan 16 11:47:51 2013
  InstallationDate: Installed on 2013-01-15 (0 days ago)
  InstallationMedia: Ubuntu 12.04.1 LTS "Precise Pangolin" - Release i386 
(20120817.3)
  MarkForUpload: True
  SourcePackage: pulseaudio
  Symptom: audio
  Symptom_Card: HDA-Intel - HDA Intel MID
  Symptom_Jack: Blue Line In, Rear
  Title: [SBC-FITPC2, Realtek ALC662 rev1, Blue Line In, Rear] Pulseaudio fails 
to detect card
  UpgradeStatus: Upgraded to quantal on 2013-01-16 (0 days ago)
  dmi.bios.date: 12/24/2009
  dmi.bios.vendor: Phoenix Technologies LTD
  dmi.bios.version: NAPA0001.86C.0000.D.0912241315
  dmi.board.name: SBC-FITPC2
  dmi.board.vendor: Intel Corporation
  dmi.board.version: 1.x
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 1
  dmi.chassis.vendor: OEM
  dmi.chassis.version: N/A
  dmi.modalias: 
dmi:bvnPhoenixTechnologiesLTD:bvrNAPA0001.86C.0000.D.0912241315:bd12/24/2009:svnCompuLab:pnSBC-FITPC2:pvrNotApplicable:rvnIntelCorporation:rnSBC-FITPC2:rvr1.x:cvnOEM:ct1:cvrN/A:
  dmi.product.name: SBC-FITPC2
  dmi.product.version: Not Applicable
  dmi.sys.vendor: CompuLab

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