I'm not sure if this helps anyone but it was the source of my issues for some of the files not being found:
http://docs.woothemes.com/document/jquery-cookie-fails-to-load/
It's possible that your webserver has outdated modsecurity rules and they are causing issues with files loading showing up properly.
The rule ID that appears to be the culprit is 950004 (or at least in my case).