They have always kept their mark up the same since the FJR first came out. When Yamaha raised their dealer price they raised their price to the customer only that same amount. When I got my '03 is was $350. The next year it reflected a hike from Yamaha to the dealers when it went to $389. It hasn't moved since and was above dealer cost by about $50. D&H has always held that ~$50 for 10 minutes worth of paper work was enough profit for them to be happy. It could very easily be higher if Yamaha raised the price again.
Did you called D&H? What is their current price? What's your source that claims that $389 was below dealer cost?