I have the same issue but for some odd reason it doesn't happen all the time. The clicking sound will start, keeps going for what seems like an eternity and will magically stop. Its been doing this for quite some time now and I'm not sure if the cause is the same as yours but since I haven't had any major issues since it started I never bothered looking for the culprit or a fix. Try to not play with your shaft so much and the clicking sound might go away.
