Comment 5 for bug 418646

I think it's some kind of power saving mechanism. I have found a notice on an archlinux wiki page about alsa where It says, that you should try to load the "snd-hda-intel" module with the option "power_save=0" by directly loading it from the commandline or by adding "options snd-hda-intel power_save=0" to the modprobe.conf file.

I couldn't test it on my machine because I have no version of Karmic installed right now, but maybe someone could give it a try.

Source: http://wiki.archlinux.org/index.php/ALSA#Pops_when_Starting_and_Stopping_Playback.3F