It's hard to come up with an answer with your description. I'll go way out on a limb here since it's my only guess at this time. If you still have the dual mass flywheel, I'd guess that it's about time to replace it. I'm guessing that it has too much play and is rattling on start up. The easiest way to tell is this: the next time that it does this, instead of shutting the engine back off, rev it up quickly. Maybe 1500 RPM and then let it come back to an idle. I mean maybe 2 or 3 seconds for the entire rev/idle cycle. If it then idles normally, it's almost certainly your flywheel. The sound that I think you're talking about is really a rattle, not an actual stutter.