You used html 5 doctype, so you have to use Html 5 elements as well such section, navbar,article, .....
lately google pays attention to these things, you can read more about it in the webmaster tools as well.Also I would suggest validating your code with http://validator.w3.org/ to making sure you do not have html error. In my view your problem is most probably the use of html5 doctype, but not using html5 structure. I suggest use html5 sections to clarify each section of your site
