i am having similar problems with my 09 aswell, but there very random. I spoke with michael at EBR today and he advised me that they are noticing these problems seem to be happening with riders who are using either a Jardine or a D&D exhaust (which i have) and that may be the problem. I don't have an idling problems, just a cough at times and a noticable flat spot at times in the rpm range. Mike advised me to take my bike to a local dealer and see what my Adaptive Fuel Value is and that the dealer can check this easily with there electronic diagnostic tool. This will help them in seeing where the problem might be and if the value is under 80 it oculd possibly be a learning to be a bit lean.
hopefully this helps some, but when i find my AFV and let EBR know we'll see if they can remap my ecm. I also was told there expecting a D&D pipe to arrive soon at EBR and there going to see how the race ecm is working with the pipe. Maybe the fuel values are off considering the RACE ecm was meant for and tuned around there old race dual outlet pipe.