I've noticed the sound difference as well, and have measured (with an infrared gun) a sginificant exhaust temp difference between the two about 3" from the head. Next time I have the Protune hooked up I'm going to see if replicate the maps between cylinders to even things out. I suspect there is a variance due to the originally intended placement of the engine in a motorcycle, where the rear cylinder could be run a bit rich to aid cooling.
