I added an extra zone underneath the quick launch, because we wanted to play with a Tree View. We decided that it was a little bit of a pain, because we would need to change the Wiki Definition and that in itself sounds like a pain. So I deleted the zone thinking that all the web parts would just disappear. It turns out they did not disappear all they did was push themselves to the bottom right zone of the page. Why that zone I have no idea...However, I am going to caution you guys against removing the web part zone without removing the web part first. You need to remove the web part before the zone or it will do some insane stuff.