I believe it's applied at shipment. I had a subscription shipment with an added item that went over $100 a few months ago and was pleasantly surprised by the shipping discount, which I hadn't even thought about, when it shipped.
Chief Technical Officer
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For non-subscription shipments, you'll see it as you check out. For subscription shipments, you should see it when you get the "is about to ship" e-mail (which is the first time we actually know for sure whether or not the order qualifies—up until then, the contents of a shipment are considered subject to change).