Have a check on this thread as I have just solved similar issues
http://www.cyclingforums.com/t-329277-15-1.html
As for the chain. I have the Ultegra 10sp and I have no issues with the chain being sensed at all. One other thing you should check is that ALL LED flashes are present.
Green = cadence
Red = speed
Orange = Chain speed (mounted on derailier)