Skype 0.92 automatically adjusts the level of the Capture channel to max, making a really unpleasant and distracting echo. I have found no way to tell it to leave my sound settings alone.
skype is a binary package, and that is probably a feature (altough a strange one that i cannot duplicate here and i have skype running all the time). You will have to report your problem in the skype forums as that is not a gentoo related issue.