Wow this is long!
Tony,
I had the same knock. It sounds like someone is under the hood hitting the engine block with a claw hammer. Sounds like the engine is going to come apart.
Like you, I took it to my dealer and had them listen. They actually admitted it had the knock, but they claimed it was "normal". "They all sound like that". "My buddy has an '03 and his does exactly the same thing".
This knock would come and go with a period of about 3 months. It would start gradually and get worse and worse until I thought any moment the pistons were going to come flying out of the block. Then mysteriously, literally overnight, it would disappear. 2 months later, it would be back again.
This happened continuously from about 5k miles to 30k miles. Then it disappeared and has not returned (47k now).
At the time, my truck was stock enough that I didn't worry. I figured that if it really did explode they'd simply give me a new engine. Now my engine has had significant modifications to the low pressure fuel system and I am convinced that if I go anywhere near a dealer they will take one look at my system and void my warranty (regardless of the time and effort I put into my design).
In my personal opinion, the knock is a "weak" injector. By "weak" I mean it's either sticking open or sticking closed. Problem is, most dealers don't have techs that are experienced enough with a "quiet" diesel to be qualified to say what's normal and what's abnormal.
So you must ask yourself: is your engine/vehicle modified enough to cause Dodge to void the warranty? You've been around here awhile and as I recall your truck is pretty close to stock. If the diesel tech you're going to see says "it's normal", then my sincere advice is to drive it and hope it grenades itself. Then they have to give you a new engine and you can say "see, I told you so".
Here's the real problem with the entire situation. The common rail injection system is sensitive to contaminants. Its components - from the CP-3 to the injector tips - are of very fine finish and materials and fit together with very tight tolerances. Since their invention it's been known that common rail injectors are particularly susceptible to fuel atomization and spray problems caused by wear at the needle and seat. We have a situation in this country where diesel fuel is not particularly "good". Cummins made the corporate decision to install 10-micron filters in the low pressure fuel system. I believe a large body of evidence (from Caterpillar and Duramax owners, among others) points to contaminants in the sub 10-micron range causing most of the damage to injector tips and injector pumps. There's always the option, then to install your own supplemental filtration system that filters down to smaller sizes.
Therein lies the problem: do you put your warranty in jeopardy by changing the stock low pressure fuel system to achieve better contaminant filtration, or do you hope contaminants smaller than 10 micron don't cause any damage so that you're not left "holding the bag" if accumulated damage finally results in an engine failure outside the 100k mile warranty? By administering the engine warranty themselves, Dodge has put every one of us between a rock and a hard place. Many Dodge dealers cannot be trusted to make proper fuel system diagnostics, and the warranty system is set up to deny coverage as often as possible. Make an effort to improve the system, lose warranty. Don't improve the system, and accumulated damage might come calling at 110k miles.
I debated this with myself for over 40k miles and 1. 5 years. I finally decided that I didn't want to leave the system stock just to get through the warranty period and end up "holding the bag" when an injector or pump went out at 120 k or 200k miles. Now, if my engine breaks, I assume I will be "on my own". But, as they say, "nothing ventured, nothing gained".
I'm not in any way advising you to swap out your low pressure fuel system. You should take some comfort knowing that I had the same issue as you and mine *appears* to have resolved itself. Guys like Coolslice were not so lucky (how many engines did he lose? 2?).
Please keep us posted!
-Ryan