I assume you are experiencing this with Karmic, aren't you? The point is that Karmic has changed a lot of things in its pulse audio configuration and you cannot anymore choose from GUI what channels to control your media keys.
The solution depends from your hardware, but you can most probably fix this by:
/usr/share/pulseaudio/alsa-mixer/paths/analog-output.conf and tweak it in order to ignore the channels you do not want to touch (in my case I wanted the media keys to only govern the PCM, so I had to exclude LFE and Master). To ignore a channel you have to set it with
volume = ignore.
alsamixer in a terminal, and set the channels you just ignored to 100%.
Hope this solves the problem for you (or at least help you to find the solution!)