For some reason, the main site is taking ages to propagate to some DNS servers.
You're probably covered by one of the servers with an (x) here: http://www.whatsmydns.net/#A/cdnjs.com
This doesn't actually affect the CDN side, which hosts the scripts.
EDIT:
For example:
http://ajax.cdnjs.com/ajax/libs/backbone.js/0.3.3/backbone-m...
http://ajax.cdnjs.com/ajax/libs/underscore.js/1.1.4/undersco...
http://ajax.cdnjs.com/ajax/libs/modernizr/1.6/modernizr-1.6....
Regardless of the reason, doesn't inspire much confidence.
Additionally, one of your links, http://ajax.cdnjs.com/ajax/libs/backbone.js/0.3.3/backbone-m... returns an XML "Access Denied" response.
Not a great start ;/
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We might have to put that one down to initial technical difficulties.
Not sure why you are getting access denied for that particular resource. May have to invalidate that object from CloudFront cache locations.
EDIT: We are using Amazon CloudFront to host the scripts.