research done at the U of MN has shown that the stain is not associated with any particular species of fungus. Instead the stain is likely a result of some compound produced by the tree to protect tissue after it is compromised in some fashion.
What actually causes the stain was undetermined by the study; the compound is broken down quickly after it is produced (the authors of the study speculate that it is a phenol that oxidizes to produce the stain, but that detail will be left to the distracted chemist to explain further).
Box Elder wood is not widely used since it is a relatively weak and rot-prone wood. But wood with the red stain is used by wood workers to make smaller, ornamental objects.