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One of the main reasons that contamination occurs after the first flush, is that the top layer of mycelium dries out and dies off. This dead mycelium is the perfect food for the contaminants (usually Trichoderma viride, the green mold) which quickly take over. The drying out of mycelium is primarily due to the developing mushrooms which tend to suck the substrate dry.
Once the first flush has finished and the mushrooms are harvested, another layer of peat-based casing is applied, which nourishes the exhausted mycelia, provides a barrier to contaminants and will result in several more healthy flushes.
I hope this helps... This technique was learned from Agaricus bisporus farming, however it may be applied to other species.
I never have trouble with my casing layer. I just pick all what's aborted and even touch the casing layer with bare hands. So far only when substrate has run out contams were visible. But that is because the shrooms were growing while they had nothing to feed themselves, aborted and were overrun by green mold. That was after the 7th or 8th flush.
Sterilize your casing layer properly and this will not happen.
The colonised grain in the jar is put in it's box in open air. The casing layer is put over it in that way 2. Never had any problems with it!
I normally bin casings after the 4th flush. You are right about air circulation too, and in essence, casing contamination is more likely if they are allowed to dry out. I recently visited a commercial Agaricus farm and they pasteurise their substrates by filling the sheds with steam.