I had a similar experience but with a different phone: the dark blue bottom of the HTC 8S turned greyish-dark-blue near the areas where it was in constant contact and friction with its black leather case. I guess it had something to do with the polycarbonate material: continual friction could be microscopically wearing down through some deformation process, which transfers some pigment onto the surface of the polycarbonate material.
I tried scrubbing it off with rubbing alcohol (40% ethyl alcohol to be exact), and I managed to reduce the discoloration - but I wasn't able to restore it to its original color. You may try your luck with it, but I suspect the process would just smudge the discoloration all over your phone so I'd be careful with this technique.:wink:
This is the reason why my current phone is Black.