This rattle/knocking that you guys describe is interesting. I experience the same sort of thing, but it comes and goes. I find it most prevalent at extremely light throttle and low RPM (900-1100). I actually don't notice it so much when it's cold, but I think that's because the engine is noisier when cold so it's masked a bit. When the engine is fully warmed, that's when I notice it when starting from a stop or at very light throttle at speed.
I hope it is just the pilot injection turning on and off.