Looking at your code there's defiantly something not right. That one div being empty should not be possible unless it was a HTML box with that code. Try adding an additional page by copying the index page before your delete it and see if the copy does the same thing? You may want to try saving your site to a new folder on your pc or as a new name and re-syncing it to see if that solves the problem.
I have no idea what that empty div is doing there. I cant find any html boxes that are empty eather when i check my design. Ive tried to copy the index page to a new page aswell, same deal there.