Where/How does WordPress pull the list for the Editor?

I ask because after doing a 2.8 upgrade, I had a bunch of extra pages showing on my editor page. I had other problems too.. such as index.php wasn’t showing correctly throug the editor. I finally went out and just deleted my database and uploaded a fresh install of my theme. I activated and then went back to my editor.

At this point, I have a brand new database and theme installed. The index.php page worked again and all other problems were fixed, except… those extra pages (which actually reside in another folder of my theme) are showing through my editor interface. How can this be?

Thoughts?