Maybe google does not like this line of .js:
$('a[rel="external"]').attr('target', '_blank');
Your setting all links to _blank, while Googlebot reads it as "_self".
For me this looks like a good reason and this could be the cause ("cloaking").
I could be wrong, but I would give it a try and remove that line of code.
@jscott: on which site do you have problems?
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