Everyone refers to the part that you installed as a damper plate, when a more accurate name is a “torsional damper plate”. That is , one of the main functions is to dampen torsional vibrations between the engine and transmission. Every
diesel engine produces torsional impulses on the crankshaft as a result of the
compression and firing stroke, and the fewer cylinders the engine has, the more noticeable the pulses are. So a six cylinder engine produces six pulses every two crankshaft revolutions, and a two cylinder engine makes two pulses every two revolutions. Therefore the pulses on the six cylinder are more closely spaced and “smoother” than the two cylinder. We normally think of a crankshaft as rotating smoothly, but in reality the crank is really twitching it’s way around, particularly at idle speed on engines with few cylinders.
When you are running your engine at idle and in neutral these pulses (twitches) are fed into the transmission and they can cause meshed gears to get into a “clatter”, where the natural
gear backlash allows one
gear tooth to rattle against its neighboring meshed gear tooth. This clatter is what you are hearing, and it might be harmful to the gear tooth, or it might be harmful to the splines on the transmission input shaft.
When you shift the transmission into gear, the
power is now fed all of the way thru the box to the shaft and prop, and the resistance of the prop against the
water pins all the gears together and gets rid of the backlash, so the clatter
noise disappears, because the backlash disappeared.
So how to fix it....? The way to resolve this problem ( not necessarily easy) is to install a torsional damper which can absorb the torsional spikes at idle but still be strong enough to transmit full engine torque at full throttle. Usually this means a damper with two or more resistances.
For example, many spring damper plates are equipped with two or three different spring strengths. Rather soft springs to soak up the torsional spikes at idle and stiffer springs to transmit full torque at w.o.t. Many manufacturers of small
marine engines use the Centa DS dampers. (DS =dual stage). Softer rubber pads to absorb torsionals at idle and more firm rubber or even pin against stop for full
power.
The selection of this ideal damper is typically the responsibility of the person or company who marries the
gearbox and the engine. If I had to guess I would say that the R&D damper which was installed is not well matched to the engine and transmission characteristics that you have. Maybe R&D can offer additional guidance.