If you live anywhere that there is light colored clay, you will understand just how much it can stain rubber and even plastic to the point harsh chemicals are necessary to remove it. Here in Oklahoma a large part of our state is red clay that stains tires horribly, even when it's a dry dust in the air.
However, because the tread, even in areas that do not make contact with the road, is largely still black, it is likely that the discoloration you were seeing is due to Tire Blooming. Check out the link Chris posted above for tire maintenance information and tips.
My tires see a lot of dirt that dries out the rubber on jobsites for work so I scrub them each wash to keep them dark and rich even before applying VRT or Tire Shine. I clean my tires with Simple Green (Diluted 2:1 if not very dirty, 1:1 for standard cleaning, full strength for very dirt tires) as I know it is biodegradable and safe and it takes quite a bit to clean the surface area on my tires so much of it winds up on the ground.