Seems to be a common complaint among many owners after the "fix".
It likely has to do with more aggressive EGR duty cycles with the software update. Boost will ramp up much more effectively once at least the high pressure EGR is told to close. It's also possible the valve isn't closing as effectively as it should or the MAF readings aren't 100%.
Could always unplug the high pressure EGR valve and go for a spin, see how much difference it makes in response.
Or, you know, a tune does fix that... though it also may void the generous extended warranty you get thanks to the court settlement.