I let mine sit for 3 weeks in storage and when I started it up, it sounded like crap for the first few seconds as the oil got around. Funny thing is, I stored my Ford Lightning pickup truck for the same amount of time alot more frequently and never had any unusual noises starting it up.
I've noticed ALL the mercedes I've owned seem to sound more and more rough as they age....even the AMG's.
I have a 2007 ML350 and actually heard the same noise two days ago. I actually stopped the car to take a look under the hood. I've also been noticing that the engine makes a wining noise on normal acceleration at low speeds.
I'm guessing it's a mix of the cold temperature and the fuel management system (i.e. fuel consumption control). I can't remember if the engine sounded the same when I first bought it. Currently have 18k miles.
If it gets worse, I'll be sure to post. For now, rest assured that others hear the same noise.