I grew the Chocolate Habanero and the Jamaican Hot Chocolate just last year. The following thread has my thoughts and experiences with the two:
http://www.thehotpepper.com/topic/17447-chocolates/
In reality, the flavors were very similar, but there were some notable differences that I could sense. But when cooked in food... you might not even notice the difference. If anything, the Jamaican Hot Chocolate might possibly give your food a slightly stronger chinense-like flavor as this flavor seemed to really stand out in mine compared to the sweeter, but more subtle tasting, Chocolate Habanero.