I was reading a thread on another forum about just this very issue quite recently Sir...
Originally I thought it was scuffing, marring or transfer of colour related to storage (possibly from a case or some such). Some folks there believed it to be due to a reaction between the finish and body chemistry, acidity from the hands you understand.
Whatever the case may be, if it does not impede the function of the firearm then I personaly wouldn't consider it all that much of an issue. None the less, I do think it may be best to go with the blued option personally if I ever were to get a BLR. I do enjoy the look of the classic bluing for most guns.
Hopefully Browning will have some answers for you.