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.

Many people have asked the question - How can I use Site Templates (Publishing Site) and keep my Document Templates, etc. up-to-date? The answer is Feature Stapling; Feature Stapling allows you to associate the desired feature to the Site Definition. Here's a good article on the topic: http://www.sharepointnutsandbolts.com/2007/05/feature-stapling.html?showComment=1213523340000.