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A plausible hypothesis a friend of mine advanced was that it's due to abnormalities in neural crest cells.
Neural crest cells are a specialized form of developmental cells unique to chordates. Unlike other cell lines which develop in fairly straightforward, position dependent ways (endoderm becomes the gut tube, ectoderm becomes the skin, neural tube becomes the brain and spinal cord, etc.), neural crest cells migrate all over the embryo, developing into all sorts of bizarre and seemingly random structures, such as teeth, inner ear, major cardiac vessels, glands, and melanocytes, the pigmented cells of the skin.
It's possible that the underlying cause of some pattern variants is altered neural crest cell migration, resulting in different distributions of pigment, but with a 'side-effect' of also altering some other migrations and developments, such as the development of the inner ear.
Of course, it's merely a plausible hypothesis, and since I'm not an embryologist by any stretch, it'll have to await testing by someone with a more appropriate skill set.
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