The way I see it, there are a number of processes that occur in a "new" system that are minimized or eliminated from a mature system. Sure, we all know about the classic nitrogen cycle that takes a few months, but that's just the tip of the iceberg. There are actually many different chemical cycles (organophosphate cycle discussion anyone?) that have to equilibrate and since many times the stabilization of these cycles has to do with live animal/ plant populations uptaking nutrients into the food chain,it can take quite a while. These subtleties are rarely discussed among hobbyists. There also has to be a fully balanced food chain developed in the tank based on your regular maintenance. Just for example, I really want stomatellas to be my primary small grazer. they reproduce well in my systems and it represents a bunch less animals I need flown in from the tropics for my tank. Stomatella don't breed any faster than stomatella breed, no matter how much you yell at them. Trust me,I know! My "new" tank is a couple of months old at this point and I'm still getting lots of swings in microalgae type/ level. I expect this from my systems because I feed at levels that produce extremely high nutrient loads periodically. The changing types and levels of microalgae growth are expected to continue until the tank fully settles in. I consider stable algae growth to be one of the best indicators of a fully balanced system. Anyway, the stomatella population has to go through a classic "boom and bust" population curve based on whatever food is currently available in the tank. Until the algae growth settles down, the stomatella population can't correctly adjust to the regular, stable food level. The result is that they (the stomatellas) are either reproducing like mad (population insufficient for available food) or starving off (reverse situation). This means sometimes (often) the microalgae is getting an upper hand and perhaps choking out coral.
This would only be a single example of how a chemical issue translates up the food chain, essentially creating multiple "ripples" in the tanks stability which have to be accommodated for by various populations. Until these populations are established, each ripple creates an instability.These ripples are almost never encountered in the wild due to the competition for anything nutritive in the ocean, and also the vast dilution factors involved. Some of these instabilities have a very real impact on the health of a coral.