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The old version of the HTML5 shim required using an InnerShiv to make HTML5 elements inserted with jQuery work properly.
But there's a new version of the shim out (released Dec 22) that fixes this. As the InnerShiv website states:
STOP! Don't use innerShiv!
html5shiv now patches for the innerHTML issue! Update html5shiv and you won't have to use innerShiv anymore: