You have to think about the newer dual-clutch systems like clutches on stick-shifts. Would you expect a new clutch to grab perfectly and without chatter the second you drop it in? Absolutely not, because the clutch material has to "cure" and the surface of both the flywheel and the clutch have to wear into each other before they'll work properly. You have the added challenge of a computer control that is set up to control a broken-in gearbox, not a brand-new one; so the computer won't tend to act quite right until everything stabilizes at the end of break-in.
And RE: the "modern cars shouldn't require break-in". They're MECHANICAL PARTS. Any mechanical parts (especially wear materials and lubricated parts) will require time to wear in. I've taken oil samples from nearly new gearboxes and the oil has been SHINY because of the break-in material wear. The gearing was in perfect condition, and ran quiet and great. All mechanical systems are NOT equal and identical set-ups will wear in differently.
2002 Focus ZX5 in Zinc Yellow: Steeda Strut Bar, Tom's Tune, Volant CAI with Aux Pipe Extension, SVT suspension, and ST200's.