I also have had the same noise since new on my truck. Alot (but not all) of the 4 and 5 cylinder engines do this. The dealer acknowledges the noise, but is reluctant to do much about it. I really don't want anyone tearing into my engine since it is fine otherwise.
Funny thing is, I have searched for this issue with the 6 cylinder version of the Atlas engine. (which I assume has the same cam drive setup) I can't seem to find the problem on the 6 cylinder engines. This makes me think it has to do with the balance shaft setup (which isn't on the 6 cylinder version).
My sisters 03 Trailblazer makes NO noise on startup, and any I have heard startup in parking lots don't make the noise either.
Here is a link http://www.355nation.net/forum/engine-d ... knock.html
and a reply from bkletke over on 355Nation forum:
Re: 2.9 start up knock
"OK, here's the latest on my start-up noise. After nearly $10,000 in reman engine and additional parts including multiple head replacements (all under warranty), GM is set to officially say that the start-up noise is not detrimental to the engine. Since they have had the truck in the shop off and on for nearly 80 days since the first of April they are prepared to give me two months of truck payments and an extended warranty for probably 3 years/45,000 miles. Officially, they can not explain to me what is causing the problem but do admit that the noise is there and it shouldn't be. They also admit that if this particular truck with only 55K miles were to be traded in, the dealership would send it to auction. They are now telling me that there will be no more repairs. They admit they don't know what is causing the noise and don't know what else to try and so are unwilling to try more ideas (throwing money at it). I've been told that GM specialists have been flown in to work on the problem and many others throughout the nation have been consulted throughout this ordeal.
My argument is: 1. I bought the truck new, paid over $20K and have paid my monthly bills faithfully, 2. I have taken outstanding care of this vehicle, 3. I did not cause the problem, and everyone involved admits it is there and shouldn't be, 4. The value of this particular truck is less than others due to the inability to repair this problem (but don't know how to establish the value loss), 5. I should not have to "eat" the value loss. 6. The replacement of the intake manifold significantly reduced the number of start-up incidents these past 2 weeks.
I have never asked for anything from GM other than to fix the truck. I have never pushed for anything other than to make my truck whole. They admit they are unable to do so. I will be pursuing a negotiated financial settlement. Will probably lose, but will pursue anyway. Any help or advice is appreciated. I apologize for the long post!
BTW - I own 3 Chevy PU's - that is all we own (63 1/2 Ton, 04 Silverado 4X4, and 06 Colorado) GM are you listening? I'm the good customer!"