Anoxic water at the bottom of the pond, typically has hydrogen sulfide gas in it. That is very toxic to fish. With a bottom aeration system, it takes that water and mixes it with the upper water column. A slow start-up will keep the toxicity levels down, and gradually mix all the water.
If your pond water gets below 40°F during the year, then the pond naturally turns over twice a year, once in the Spring, and once again in the Fall. I have started my aeration system up without the "15 minute and double it every day" rule when the surface water temp was in the low 40's in the Spring without any problems. (I use my pond for tests, I would never do that in a clients pond.) If the water was warmer than that, I wouldn't chance it, and I wouldn't chance doing it in the Fall unless the surface water was in the upper 30's and then it would be the winter diffuser only.
Thanks! I figured it was something to do with chemical/gas states in the water. We fortunately haven't had much of a problem with algae blooming and dying -yet. There still has to be quite a bit of organic crud on the bottom.
