I have the same problem. My Motherboard is a MSI H55M-E33.
The output of alsa-info.sh is at 
http://www.alsa-project.org/db/?f=63c740f53e7c7e48b2e6fd03d7b70fc98f6ad688

If I use gnome-alsa-mixer I can set the volume of the front panel jack
(headphones) and the rear jack (speakers) seperatly, using the "front"
and "side" sliders, but the mute button of any of these mutes master
too.

Philip

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HDA ATI SB Realtek ALC889 - does not mute when headphone plugged in front
https://bugs.launchpad.net/bugs/557015
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