Wow that is something else, guess I'd be worried about My good cues too if that were to happen to me. My personal cues stay in a case in between uses, and I've never had that happen. A yellowing finish possibly, but not a splotchy shaft like that.
I really don't have a clue what caused It either. I read most of the thoughts here, and most seem plausable, so I could be drawn into them too, but The one that caught My attention the most was the bleach, but only because I have seen a reaction simular before with It, and It was a splotchy rust color, as if a rusty bolt was added to the mix. The difference was It was'nt on a shaft, and didn't take that long to develop, so that may not be what It is, and if by chance another shaft from a different maker has the same marks then I would be concerned with Your good cue, and keep It in a different case just to be safe. Greg