The blue stain is a fungus.  It lives off the easily available wood sugars and does not degrade the cellulose, lignin, and hemicellulose. 

A fungus cannot grow at a temperature above 120F.  The growth rate begins to slow above 90F.  If you get the wood in the kiln and heat it quickly to a wet-bulb temperature greater than 120F, the stain will not grow in the kiln.

Left outside at a lower temperature, say 80F to 90F, the stain will rapidly propagate through the sapwood.  The same thing could happen in a low temperature kiln, although southern pine would not be dried that way.

As far as mixing it with other wood, two things come to mind.  You are either mixing lumber from old logs with lumber from fresher logs or you are mixing lumber that has sat around with freshly-sawn lumber.  Either way there is likely to be moisture variability between the two types of wood.  The other thing is that the blue stain does increase the wood permeability a little bit and probably makes it dry a little faster.  This might also contribute to variability at the planner.