From the article:
One disheartening result was that our package received more abuse when marked "Fragile" or "This Side Up." The carriers flipped the package more, and it registered above-average acceleration spikes during trips for which we requested careful treatment.
(the comments on the article are full of examples as well)
Sidenote: Paul and I came up with a similar idea for an experiment last year to send an accelerometer with a GPS module in a parcel around the world and see what the readouts would be. Never came to it, so we are glad Popular Mechanics did this test for us!