Preventing stain in the upcoming hotter months is important so the wood next fall and winter is free of stain.  Mills tend to have to store logs for fire season and excessive log storage often results in logs prone to stain.  Log rotation - first in, first out - is important.  This probably means extra work in moving the sprinklers so you can get to the earlier decks.  Using sprinklers does help reduce the potential for stain.  Keeping the log surface wet makes it more difficult for a fungus to grow (because the high MC restricts oxygen).  The whole log surface, including the ends, should be wet.  Sprinklng also helps keep logs cooler (chemical reactions happen faster at higher temperatures).   Fungi are associated with the blue stain in pine and the black discoloration in Douglas-fir sapwood.  Chemicals are involved in brown stain and sticker stains.

Once you have the potential for brown stain due a longer log storage or higher storage temperatures, here are some kiln suggestions.

Higher airflow should help.  Overloading the kiln will hurt.  Avoiding steam spray almost always helps.  Lower temperature early is effective for pine, but I’m not sure if it works for hemlock (any comments on this?).  A lower humidity early should help.  A lower final temperature usually helps, but this slows things down a lot.  Think of it this way – the liquid water early in drying moves the bad chemicals to the surface.  The higher temperature later in drying causes the bad chemicals to change color.  Getting the surface to dry quickly prevents the liquid water from carrying the chemicals to the surface and concentrating there.

The black growth on the outside and the blue stain are probably different fungi, but the following appies to both.

Fungi do not grow at temperatures above about 100 or 120F.  Peak growth is at about 80F.  During most normal softwood schedules the fungus will not grow after the wood is put in the kiln and the kiln is started.  You could probably help it grow by putting a charge into a warm kiln and not starting it for a day or two.

Most normal softwood schedules reach high enough temperatures (>150F) to kiln all hyphae (the bodies of the fungus).  The spores (similar to eggs) of the fungi may also be killed.  There's insufficient time during kiln startup for blue stain to grow.  It was in the rough green lumber if it shows up at the planer.  Log and lumber storage practices should be reviewed.

Kiln dried lumber then contains dead hyphae, probably dead spores, and maybe some living spores (this depends on fungus species and might be a conservative statement for southern pine drying).  Spores do not germinate unles there is free water present meaning the wood needs to be above 25 to 30% MC.  Certainly, fungi do not grow on wood under 20% MC.

New spores fall from the air onto the wood immediately after it is pulled from the kiln, so living or dead spores after drying really doesn't matter.  These spores grow if the wood gets rewetted. 

Keep dry wood dry.  Keep it out of the rain, especially if it solid piled after planing.  Wrapping wood that is at a high mc (even if it meets grade) can sometimes result in condensation on the wrap that leads to localized areas of high MC.  The fungus can grow.  By the time the wrap is removed the water has left anf it can appear that the fungus grew on dry wood.

Keep the mill area clean and free of any rotting debris to reduce the spores in the air.  Sprinkling logs helps too on the blue stain.