Mine does the same thing. Switch the hoses side to side to make sure the left slider in the Carbtune isn't hanging up slightly. I think you'll find the right side is still different....
Check how well they rise together if you slowly increase the throttle - the right will probably jump a bit but follow the left pretty closely.
I'd be interested in the answer to this as well. My bike runs well and I'm happy, but the right pipe still tends to discolor a bit, and the right pilot screw is almost a full turn out more than the left. What is it about the right cylinder on these engines?
