I have a very similar problem. Unfortunately, ive not managed to find out what it is yet.
Mine seems to do it at extreme tempretures, i.e first thing in the morning below 5 degrees or it was doing it in the summer when it was 25 degrees plus. Makes me think mine could be a sensor issue but its been in to the dealers probably 6 times and they cant seem to diagnose it.
My other thought is maybe fuel pump because mine seems to be rough on idle (Intermittently) and rough between 1200 - 1600 rpm (Again intermittently). But drives fine after 15 - 20 minutes.
Its doing my head in!
VW have changed the flywheel under warranty because they thought it was that.
Sorry i cant be of more assistance but im interested to see what anyone else thinks it could be.