In the horse world, when you breed two Overo paints together, there's about the same % chance that the foal will be a lethal white as with roan guineas. I wonder if it's caused by the same gene?
I'm not sure if it's the same gene, but these disorders show up in several animals (horses, humans, hamsters, rats, dogs, cats, ferrets, guinea pigs) and they all involve a particular embryonic development problem, as far as I know. There's not much research on the problem in guinea pigs, but more on other animals. (broken link removed) is a summary of the megacolon problem in rats, for instance.
Basically, nerves develop in a tube down the back of the embryo. Certain chemicals trigger the migration of neurons from the neural tube to the rest of the body. If any of these chemicals are suppressed or delayed, it can result in a delay in neuron migration. The pigment cells migrate too. If they're late, they can't migrate across the entire body and therefore can't pigment all the hair--when an animal has one copy of the allele of whatever gene causes this, enough pigment gets out to create the roan or dalmatian pattern. (Other genes modify how spotty the pig is. Maybe this is why breeders will breed dal x dal, because they can't see the spottiness genes on a self pig.) Typically, the head will have more color and less roaning, and sometimes the rear will be colored as well, as with (broken link removed). This is because the delayed pigment cells can't get as far from the two openings of the neural tube, one at the head and one at the "tail". In Dalmatian dogs, neurons and pigment cells are linked so much that dogs with colored patches on their ears are less likely to be deaf than those with entirely white ears.
In lethals, this entire mechanism is turned off. Obviously some other mechanism can get nerves to some places they need to go, but the absence of pigment cells somehow prevents the normal development of eyes, teeth, and sometimes ears in guinea pigs. In rats, the associated neurons often fail to reach the colon, making it impossible for it to function properly. I don't know if this is related to the digestive problems in pigs--could someone find a detailed report of one or more of these necropsies?