The boxes you see are added by the editor in Acrobat. They are not in the actual PDF file. Acrobat is trying to be smart about what might belong together, based on how content is organized and positioned on a page. Sometimes this does get in the way, and I am not aware of any way around this (besides going back to a really old version of Acrobat that does not do that like Acrobat 9). This also means you don't have any control over this.