Same Problem
I have a 2010 Golf TDI & it has the wierd hiccup thing, too. I have a manual transmission. When it hiccups I'm usually accelerating from a stop & have my foot completely off the clutch. It's like the car dies for a fraction of a second then decides to run again. I've also had it die on me a couple of times as I coast to a stoplight or stop sign in neutral. On top of that, my car creaks & rattles like a 15 year old car...it is VERY annoying. The tech at the dealership was shocked at the amount of noises inside.
As far as the hiccup goes, they updated the engine software to try to cure it, but it didn't work. My car was manufactured in March if that is of any interest...apparently there was an update released for the engine in the last couple of months...it improved my mileage from 38 mpg/hwy to 44 mpg/hwy. Now getting 40-ish on most of my trips around town in combined driving.