You have quite a lot of invalid HTML in your includes files (div tags in the header insert for example (header insert is between the <head> tags, whereas the default header is for content above the forum)); please remove everything (even things that appear valid) from the HTML Includes page (yours is
here) and see if the JavaScript libraries load properly.
You should also be using quotes ("") vs apostrophes ('') in your html coding. Additionally, you should also get the latest google analytics code; what you're using doesn't appear to be their current coding.
It's also good form to add your JavaScript before the </body> tag, which would go in the "Default Footer".