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Re:Amazon Free Shipping minimum is now $49 by jbkkd on Monday February 22, 2016 @12:25AM (#11148692)
I have a business that purchases multiple items in a single order on a daily basis, and have never encountered this. We always get free shipping for orders, even if boxes are split.

I'm curious about your use case, were they non amazon fullfiled items?

Re:Amazon Free Shipping minimum is now $49 by deftnerd on Monday February 22, 2016 @12:36AM (#11148743)
Answered in detail above, but to sum it up, all the items were either Amazon supplied or FBA, so they would ship directly from an Amazon warehouse.
Re:Amazon Free Shipping minimum is now $49 by tdeck on Monday February 22, 2016 @01:16AM (#11148916)
The paranoid engineer in me thinks this "box shuffling" is a feature flagged behavior and you ended up in an unlucky bucket.
Re:Amazon Free Shipping minimum is now $49 by jlgaddis on Tuesday February 23, 2016 @03:53AM (#11157491)
I can't recall exactly where the option is but I do remember seeing an option that offered a choice between "ship my items as fast as possible, even if it means multiple, separate shipments" versus "put everything into the same shipment, even if it means it might take a little longer".