The nunchuks in our house (both for combat and for our Wii) have stayed the original color at which we purchased them. No fading, no problems with them on our end. We didn't leave them sitting on a window ledge or something for 95% of their lifespan, so we're confident they're still the same as they were on day one.
And, these nunchuks pictured above aren't as old as ours, recently purchased before the Christmas holiday. But, as the peripherals were played with for hours on end by the lucky recipients, they started to change color. Interesting. And, more people over at the Nintendo forums are reporting the same thing.
Any of you having this problem yourselves?