I recently ran into a problem where when I went to edit-mode of my page the number of zone would change. In view mode I had 4 zones and in edit mode i only had two. This is in a MOSS Publishing site and my first thought was that it had been edited in SharePoint Designer. After confirming that that was not the case, I discovered that someone added zones directly to the content page in the “pages” library, rather than to the underlying layout page in the master page gallery. I was able to quickly resolve the issue. Hope this helps.