This isn't the first time I've heard of this problem - Craig, who writes our DS homebrew round-ups, is 'blessed' with a DS that has the same problem. I don't think there's anything you can do to fix it, so my best suggestion would be to contact Nintendo to sort out a repair/replacement. I'm told that out-of-warranty repairs cost a flat fee of £35 regardless of the issue which, while not exactly cheap, is certainly cheaper than getting a new DS.
I wonder how common it really is... it's a real shame, given how essential accurate calibration really is
E