Unfortunately the native install has various problems with the alsa sound driver, so it is sometimes easier to install and run under wine/cedega with some sound cards. It was fine when I had the old SB128, but lot's o' trouble with most onboard or non creative sound systems...
So I deleted my native install and run it with cedega now... It's also the only good way to run quake2, otherwise you have endless mouse cursor and sound issues...