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Audio hiccups

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Hello,
I found an encoding that looks like is not well supported in xbmc or raspberry, using raspbmc.
I own some tvshows encoded in a really compressed setting, in each of these episodes, the audio jitters, hiccups and makes a lot of strange digital noises during playback, the files reside on a synology NAS, nfs exported, if I mount them on my linux laptop and play using mplayer or vlc, the files playback without a problem, with a good audio quality (at least without hiccups! ^_^).

The raspberry has both VC-1 and mpg2 codecs bought and installed.

Video plays perfectly.

Here I'm attaching the xbmc.log in debug mode during playback,the mediainfo of the file and a sample file (splitted the first minute).

Is there a way to understand why it playbacks audio like that? Could be workarounded or fixed?

A big thank you for the answer and let me know if I could be of any help. ^_^

-------------MOD EDIT: REMOVED LOG SPAM ----------------

Code:
$ mediainfo Cyborg009.1x01.mp4
General
Complete name                            : Cyborg009.1x01.mp4
Format                                   : MPEG-4
Format profile                           : Base Media / Version 2
Codec ID                                 : mp42
File size                                : 87.0 MiB
Duration                                 : 23mn 22s
Overall bit rate mode                    : Variable
Overall bit rate                         : 520 Kbps
Movie name                               : 01
Encoded date                             : UTC 2013-07-04 02:54:13
Tagged date                              : UTC 2013-07-04 03:05:09
Writing application                      : HandBrake rev0 2013051899

Video
ID                                       : 1
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : Main@L3.0
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 4 frames
Codec ID                                 : avc1
Codec ID/Info                            : Advanced Video Coding
Duration                                 : 23mn 22s
Bit rate mode                            : Variable
Bit rate                                 : 452 Kbps
Width                                    : 640 pixels
Height                                   : 480 pixels
Display aspect ratio                     : 4:3
Frame rate mode                          : Constant
Frame rate                               : 25.000 fps
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Progressive
Bits/(Pixel*Frame)                       : 0.059
Stream size                              : 75.6 MiB (87%)
Writing library                          : x264 core 130 r2273 b3065e6
Encoding settings                        : cabac=1 / ref=1 / deblock=1:0:0 / analyse=0x1:0x111 / me=hex / subme=2 / psy=1 / psy_rd=1,00:0,00 / mixed_ref=0 / me_range=16 / chroma_me=1 / trellis=0 / 8x8dct=0 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=0 / threads=6 / lookahead_threads=2 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 / b_adapt=1 / b_bias=0 / direct=1 / weightb=1 / open_gop=0 / weightp=1 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=10 / rc=2pass / mbtree=1 / bitrate=452 / ratetol=1,0 / qcomp=0,60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20,0 / qblur=0,5 / ip_ratio=1,40 / aq=1:1,00
Encoded date                             : UTC 2013-07-04 02:54:13
Tagged date                              : UTC 2013-07-04 03:05:09
Color primaries                          : BT.601 PAL
Transfer characteristics                 : BT.709
Matrix coefficients                      : BT.601

Audio
ID                                       : 2
Format                                   : AAC
Format/Info                              : Advanced Audio Codec
Format profile                           : LC
Codec ID                                 : 40
Duration                                 : 23mn 22s
Bit rate mode                            : Variable
Bit rate                                 : 63.9 Kbps
Maximum bit rate                         : 120 Kbps
Channel(s)                               : 1 channel
Channel positions                        : Front: C
Sampling rate                            : 48.0 KHz
Compression mode                         : Lossy
Delay relative to video                  : 80ms
Stream size                              : 10.7 MiB (12%)
Encoded date                             : UTC 2013-07-04 02:54:13
Tagged date                              : UTC 2013-07-04 03:05:09

Code:
$ ffmpeg -acodec copy -vcodec copy -ss 00:00:00 -t 00:01:00 -i Cyborg009.1x01.mp4 sample.mp4
WARNING: gnome-keyring:: couldn't connect to: /home/gabrieletassoni/.cache/keyring-vCNAye/pkcs11: No such file or directory
ffmpeg version 0.8.6-6:0.8.6-1ubuntu2, Copyright (c) 2000-2013 the Libav developers
  built on Mar 30 2013 22:20:06 with gcc 4.7.2
*** THIS PROGRAM IS DEPRECATED ***
This program is only provided for compatibility and will be removed in a future release. Please use avconv instead.
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'Cyborg009.1x01.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42isomavc1
    creation_time   : 2013-07-04 02:54:13
    title           : 01
    encoder         : HandBrake rev0 2013051899
  Duration: 00:23:22.88, start: 0.000000, bitrate: 520 kb/s
    Stream #0.0(und): Video: h264 (Main), yuv420p, 640x480 [PAR 1:1 DAR 4:3], 451 kb/s, 25 fps, 25 tbr, 90k tbn, 50 tbc
    Metadata:
      creation_time   : 2013-07-04 02:54:13
    Stream #0.1(und): Audio: aac, 48000 Hz, mono, s16, 63 kb/s
    Metadata:
      creation_time   : 2013-07-04 02:54:13
Output #0, mp4, to 'sample.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42isomavc1
    creation_time   : 2013-07-04 02:54:13
    title           : 01
    encoder         : Lavf53.21.1
    Stream #0.0(und): Video: ![0][0][0] / 0x0021, yuv420p, 640x480 [PAR 1:1 DAR 4:3], q=2-31, 451 kb/s, 25 tbn, 25 tbc
    Metadata:
      creation_time   : 2013-07-04 02:54:13
    Stream #0.1(und): Audio: aac, 48000 Hz, mono, 63 kb/s
    Metadata:
      creation_time   : 2013-07-04 02:54:13
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1
Press ctrl-c to stop encoding
frame= 1499 fps=487 q=-1.0 Lsize=    4724kB time=59.88 bitrate= 646.2kbits/s    
video:4210kB audio:469kB global headers:0kB muxing overhead 0.955674%

Sample file: https://docs.google.com/file/d/0BzOZ0GC2...sp=sharing

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