I had a similar problem when I was making a lot of edits to my layout for controlcards and digital library records.
The problem for us was that while editing, we did not nest the <div> tags properly so page elements were not closing out (</div>) correctly and running into each other.
So I would double check that the opening and closing div tags are in the right place and that there are the right number of them.
Chrome has a developer tools built right in under the view menu that allow you to look at a page and see exactly which elements are in play for different parts of a page. Firefox too has a developer plugin for this purpose. Here is a screen shot:http://people.carleton.edu/~nwilson/list/devview.png
This may help you ID if your divs or other elements are nested improperly.