I just looked over both the '09 and '10 manuals, which are higher grade PDF's than the older ones, and it is clear (at 400% enlargement) that the seal is illustrated with the open side (the side with the spring loaded lip) installed facing the crank. I am certain that I've seen them installed this way, but I've also seen them the other way 'round. It appears that Yamaha considers it correct, although if the interest was purely in sealing the oil pressure into the passage, it would be the other way around. But obviously, there is no harm in having oil "leak into" the primary case, so the engineers may have deliberately called for this in order to have the resulting leak serve to lubricate the seal and reduce the wear to it. In so doing, they must have determined that the oil pump will provide adequate volume and pressure to the system in spite of the loss, and it may even have been a way to limit pressure.