OP never got back with his problem. Have you checked the plugs? Sometimes they do go bad. You need to be sure that you have spark on both cyl. Check both ends of the plug wires and if you can swap the wires and see if the problem goes to the other cyl. Once you are sure the plugs and wires are good get back to us or go to the self help section for testing the coil. Since your bike is still under warrenty you need to call the dealer to see if he wants to pick it up and check it in the shop.