did you toggle the "IEC958 Playback Switch" ?

can you post the output of alsa-info.sh

https://wiki.ubuntu.com/Audio/AlsaInfo


http://www.realtek.com/products/productsView.aspx?Langid=1&PNid=24&PFid=37&Level=5&Conn=4&ProdID=165

The ALC663 is a 5.1 Channel High Definition Audio Codec

The ALC663 provides two independent S/PDIF outputs and supports
16/20/24-bit SPDIF output with a sampling rate of up to 192kHz, offering
easy connection of PCs to high quality consumer electronic products such
as digital decoders and speakers. In addition to the standard (primary)
SPDIF output function, the ALC663 features another independent
(secondary) SPDIF-OUT output and converters that transport digital audio
output to a High Definition Media Interface (HDMI) transmitter (becoming
more common in high-end PCs).

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to alsa-driver in Ubuntu.
https://bugs.launchpad.net/bugs/1259070

Title:
   N90SV, Realtek ALC663, Mic, Internal  Underruns, dropouts or
  crackling sound

Status in “alsa-driver” package in Ubuntu:
  Incomplete

Bug description:
  Recording directly with arecord works, but using pulseaudio has
  crackling noise.

  Workaround is to disable timer based scheduling in /etc/pulse/default.pa
  AND setting

  default-fragments = 4
  default-fragment-size-msec = 90 (or higher, lower still produces noise)

  in daemon.conf. Total hw buffer size is 371 ms (according to
  pulseaudio -vvv > pulse.log)

  ProblemType: Bug
  DistroRelease: Ubuntu 13.10
  Package: alsa-base 1.0.25+dfsg-0ubuntu4
  ProcVersionSignature: Ubuntu 3.11.0-15.22-generic 3.11.10
  Uname: Linux 3.11.0-15-generic i686
  ApportVersion: 2.12.5-0ubuntu2.1
  Architecture: i386
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  martin     2432 F.... pulseaudio
  Date: Mon Dec  9 09:29:29 2013
  InstallationDate: Installed on 2013-04-22 (230 days ago)
  InstallationMedia: Kubuntu 12.10 "Quantal Quetzal" - Release i386 (20121017.1)
  MarkForUpload: True
  PackageArchitecture: all
  SourcePackage: alsa-driver
  Symptom: audio
  Symptom_AlsaRecordingTest: ALSA recording test through plughw:SIS966 failed
  Symptom_Card: Internes Audio - HDA SIS966
  Symptom_Jack: Mic, Internal
  Symptom_Type: Underruns, dropouts, or "crackling" sound
  Title: [N90SV, Realtek ALC663, Mic, Internal] Underruns, dropouts or 
crackling sound
  UpgradeStatus: Upgraded to saucy on 2013-10-18 (51 days ago)
  dmi.bios.date: 02/25/2010
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: 207
  dmi.board.asset.tag: ATN12345678901234567
  dmi.board.name: N90SV
  dmi.board.vendor: ASUS CORPORATION
  dmi.board.version: 1.0
  dmi.chassis.type: 10
  dmi.chassis.vendor: ASUSTeK Computer Inc.
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvr207:bd02/25/2010:svnASUSTeKComputerInc.:pnN90SV:pvr1.0:rvnASUSCORPORATION:rnN90SV:rvr1.0:cvnASUSTeKComputerInc.:ct10:cvr:
  dmi.product.name: N90SV
  dmi.product.version: 1.0
  dmi.sys.vendor: ASUSTeK Computer Inc.
  mtime.conffile..etc.modprobe.d.alsa.base.conf: 2013-12-08T17:23:33.527378

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