Same problem here, although the gnome gui turns automatically the PCM
level to 100% (using on board AC97 here), which also results in
incredibly annoying high frequency noise.

my amixer output:

Simple mixer control 'Master',0
  Capabilities: pvolume pvolume-joined pswitch pswitch-joined
  Playback channels: Mono
  Limits: Playback 0 - 31
  Mono: Playback 12 [39%] [-28.50dB] [on]
Simple mixer control 'Headphone',0
  Capabilities: pswitch
  Playback channels: Front Left - Front Right
  Mono:
  Front Left: Playback [on]
  Front Right: Playback [on]
Simple mixer control 'PCM',0
  Capabilities: pvolume
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 255
  Mono:
  Front Left: Playback 243 [95%] [-2.40dB]
  Front Right: Playback 243 [95%] [-2.40dB]
Simple mixer control 'Front',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 12 [39%] [-28.50dB] [on]
  Front Right: Playback 9 [29%] [-33.00dB] [on]
Simple mixer control 'Front Mic',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 20 [65%] [-4.50dB] [off]
  Front Right: Playback 20 [65%] [-4.50dB] [off]
Simple mixer control 'Front Mic Boost',0
  Capabilities: volume
  Playback channels: Front Left - Front Right
  Capture channels: Front Left - Front Right
  Limits: 0 - 3
  Front Left: 2 [67%]
  Front Right: 2 [67%]
Simple mixer control 'Surround',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 11 [35%] [-30.00dB] [on]
  Front Right: Playback 9 [29%] [-33.00dB] [on]
Simple mixer control 'Center',0
  Capabilities: pvolume pvolume-joined pswitch pswitch-joined
  Playback channels: Mono
  Limits: Playback 0 - 31
  Mono: Playback 31 [100%] [0.00dB] [on]
Simple mixer control 'LFE',0
  Capabilities: pvolume pvolume-joined pswitch pswitch-joined
  Playback channels: Mono
  Limits: Playback 0 - 31
  Mono: Playback 30 [97%] [-1.50dB] [on]
Simple mixer control 'Side',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 31 [100%] [0.00dB] [on]
  Front Right: Playback 31 [100%] [0.00dB] [on]
Simple mixer control 'Line',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 27 [87%] [6.00dB] [off]
  Front Right: Playback 27 [87%] [6.00dB] [off]
Simple mixer control 'CD',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 0 [0%] [-34.50dB] [off]
  Front Right: Playback 0 [0%] [-34.50dB] [off]
Simple mixer control 'Mic',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 0 [0%] [-34.50dB] [off]
  Front Right: Playback 0 [0%] [-34.50dB] [off]
Simple mixer control 'Mic Boost',0
  Capabilities: volume
  Playback channels: Front Left - Front Right
  Capture channels: Front Left - Front Right
  Limits: 0 - 3
  Front Left: 0 [0%]
  Front Right: 0 [0%]
Simple mixer control 'IEC958',0
  Capabilities: pswitch pswitch-joined cswitch cswitch-joined
  Playback channels: Mono
  Capture channels: Mono
  Mono: Playback [off] Capture [on]
Simple mixer control 'IEC958 Default PCM',0
  Capabilities: pswitch pswitch-joined
  Playback channels: Mono
  Mono: Playback [off]
Simple mixer control 'Capture',0
  Capabilities: cvolume cswitch
  Capture channels: Front Left - Front Right
  Limits: Capture 0 - 31
  Front Left: Capture 21 [68%] [15.00dB] [off]
  Front Right: Capture 21 [68%] [15.00dB] [off]
Simple mixer control 'Capture',1
  Capabilities: cvolume cswitch
  Capture channels: Front Left - Front Right
  Limits: Capture 0 - 31
  Front Left: Capture 0 [0%] [-16.50dB] [off]
  Front Right: Capture 0 [0%] [-16.50dB] [off]
Simple mixer control 'Beep',0
  Capabilities: pvolume pswitch
  Playback channels: Front Left - Front Right
  Limits: Playback 0 - 31
  Mono:
  Front Left: Playback 0 [0%] [-34.50dB] [off]
  Front Right: Playback 0 [0%] [-34.50dB] [off]
Simple mixer control 'Channel Mode',0
  Capabilities: enum
  Items: '6ch' '8ch'
  Item0: '8ch'
Simple mixer control 'Digital',0
  Capabilities: cvolume
  Capture channels: Front Left - Front Right
  Limits: Capture 0 - 120
  Front Left: Capture 90 [75%] [15.00dB]
  Front Right: Capture 90 [75%] [15.00dB]
Simple mixer control 'Input Source',0
  Capabilities: cenum
  Items: 'Mic' 'Front Mic' 'Line' 'CD'
  Item0: 'Mic'
Simple mixer control 'Input Source',1
  Capabilities: cenum
  Items: 'Mic' 'Front Mic' 'Line' 'CD'
  Item0: 'Mic'

lsmod |grep snd (also shows my usb webcam with integrated mic)

snd_hda_codec_realtek   203328  1 
snd_hda_intel          26920  6 
snd_hda_codec          75708  2 snd_hda_codec_realtek,snd_hda_intel
snd_pcm_oss            37920  0 
snd_mixer_oss          16028  1 snd_pcm_oss
snd_usb_audio          84224  2 
snd_usb_lib            16284  1 snd_usb_audio
snd_pcm                75296  7 
snd_hda_intel,snd_hda_codec,snd_pcm_oss,snd_usb_audio
snd_seq_dummy           2656  0 
snd_seq_oss            28576  0 
snd_seq_midi            6432  0 
snd_seq_midi_event      6940  2 snd_seq_oss,snd_seq_midi
snd_seq                50224  6 
snd_seq_dummy,snd_seq_oss,snd_seq_midi,snd_seq_midi_event
snd_rawmidi            22208  2 snd_usb_lib,snd_seq_midi
snd_hwdep               7200  2 snd_hda_codec,snd_usb_audio
snd_timer              22276  2 snd_pcm,snd_seq
snd_seq_device          6920  5 
snd_seq_dummy,snd_seq_oss,snd_seq_midi,snd_seq,snd_rawmidi
snd                    59204  26 
snd_hda_codec_realtek,snd_hda_intel,snd_hda_codec,snd_pcm_oss,snd_mixer_oss,snd_usb_audio,snd_pcm,snd_seq_oss,snd_seq,snd_rawmidi,snd_hwdep,snd_timer,snd_seq_device
soundcore               7264  1 snd
snd_page_alloc          9156  2 snd_hda_intel,snd_pcm

-- 
PCM control in ALSA set to 10% no matter what GUI volume control is
https://bugs.launchpad.net/bugs/485530
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