Because of the stresses introduced into the barrel during the fluting process, I believe. Having a barrel fluted after the rifling is cut may not affect the initial accuracy, but it could make the barrel act all funny once it starts to get hot.
I'm no barrel maker, I'm just parroting what I've been told. If you want a fluted barrel, it's best to get one that was fluted before the rifling is cut. First flute, then rifle, then stress relieve.
Personally, I think that flutes look cool, but on an overall, I think I've had better accuracy from non fluted barrels on an overall. To my way of thinking, getting a pipe to spit a projectile to the same point of impact every time is hard enough to do as it is; so why go complicating it with something that could have an adverse effect on accuracy.