Do you have a sound card like Intel Corporation 82801DB/DBL/DBM (ICH4/ICH4-L/ICH4-M) AC'97 Audio Controller and ALSA master volume doesn't work?
Some cards are using ALSA Headphone Volume to control "Master Volume". ALSA developers had put an option in module snd_intel8x0 to workaround this issue. Just put this line in /etc/modprobe.conf:
options snd_intel8x0 ac97_quirk=hp_only
So, next time module is loaded you have Master Volume where is suppose to be. Ah, you must reconfigure your mixer settings.
More info/options in:
or ALSA documentation.