Comment 2 for bug 788540

I am also experiencing this behavior on my Thinkpad T410 running Kubuntu 11.04. The hardware and software indicators can get reversed either by toggling the mute on the panel icon or if the hardware mute is enabled on boot or resume from suspend. Pressing the mute button switches both indicators, keeping them reversed. Changing the volume via the hardware buttons will reset the hardware mute indicator and get them back in sync.

I rebooted into the stock Windows 7 install to check its behavior. It functions in a much more logical way: the software and hardware mute indicators are kept in sync at all times.

While it is true that it is desirable at times to disable the speakers while leaving the headphones operable, IMHO the current behavior is not the correct way to expose this functionality to the user.