Uh oh, you probably didn't change the o-rings in the dip tubes and the lid did you? That is probably the source of your problem. Run out and get yourself a rebuild kit right away.
I would otherwise be surprised if the stainless steel in the rest of the keg couldn't get clean enough. May still need some more elbow grease to get it really right though.
I am not drunk! I am by nature a loud, friendly, clumsy person!