You're right, it appears to be busted. You'll mostly likely need to revert and redo your footer template. How many custom templates are you running? 3.0.x to 3.6.2 is a pretty major upgrade, and you'll lose quite bit of 3.6's added functionality if you don't update the templates, not to mention running into the occasional glitch.
Personally, I would work off a clean default template, and reinstitute the theme changes from there, just to make sure your theme is fully 3.6 compatible.
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