I have seen dark spots stained onto wild black cherry, white oak and poplar. I think, or at least it appears to me that this is something in the piece of wood. I say this because I have seen these stains on wood I have split for firewood and it has never came in contact with a mill. It has a strong odor and it is purple in color when it is fresh. It is also more than "skin deep" so to speak. Some of the cherry I have worked with I used with the stain, figuring it would surely just be on the surface and sand right out and I was wrong.
We could be talking about different things here, I have seen light stain marks from what appeared to be the band mill blade and those do sand out and do not have that terrible chemical odor. As far as lube, I mix some Simple Green in my water tank and set it to just give a steady drip onto the blade. I run it this way for all wood I mill and haven't had any problems. Some folks say Pine-Sol works better for sappy pine logs, but I have had no trouble or reason to switch from the Simple Green stuff.
I always used to think if it was a cleaner and it had a color in the name it wouldn't work...Simple Green, Fast Orange, Happy Yellow, etc. Glad I found a use for one of them.

Edit: I have seen this strange purple stain on wood many times and I cannot connect it to anything, time of year, area the tree was from, type of soil, etc. It didn't matter.