Didn't Nick tune your truck ???
If you are having problems with a rattle at low rpms it is most likely fuel pressure.
The tables are different for Federal, North East, and CA emissions trucks due to the EGR and air pump.
If you are running scripts for tunes you need to make sure things are not getting changed that should not be, scripts are indiscriminate, they do not care what they change.
If it is in one specific area you can make a MAP file and it will show you what is going on and what cells it is happening in as well as the frequency, etc.
If it's your own tuning go back to stock and drive the truck, if it goes away then change one thing at a time until the problem comes back.
Good Luck.