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WilliamThe final assembly of a baseball includes a layer of contact cement on the leather and the winding. More often than not, when you see a spot forming on the ball it has to do with a chemical reaction inside the ball. Depending on the age, it could also be staining that shows itself late in life due to factory processes. I've read that the horrible toning issues that Rawlings experienced in the 80's was caused by the Haitian factory that they were made in using regular water to soak the hides instead of distilled water.
The myth that if you keep a baseball in the dark it will be fresh forever is false. Toning is completely natural. Nothing stays pure white forever. Keeping the signature out of UV light will help the ink from fading. However, I'm not convinced that there isn't a chemical element to fading ink. In those cases, fading, bleeding, or downright disappearing acts will happen.
I've taken a zen-like approach to baseballs lately. Do what you can, just enjoy them.