Well yes, if you look at their map they put 10's in the 0% throttle area trying to make up for the stall.

This doesn't work and will cause a gigantic hot start problem, load up the combustion chamber, spark plug and pipe with black soot. I don't have my map in front of me, but I can get you started in the right direction.
So the first thing you want to do is turn off the autotune. Next select the 0% column and zero it out. Next select 2500 to 9000 rpm at 0% throttle and set to 1. 3250rpm to 9000 at 2% throttle set to 1. Open powercommander tools>features> check accel pump. Start with 2% trigger at 33 rpm and 10% fuel (might need more fuel). Any negative number in the 80 to 100% throttle area should be no less than a zero. Also study your fuel map, if you see a "3" in the middle of two "10's", obviously their was a lambda fart and should be averaged. If you wish to return to autotune, deselect the accel pump.
I think if you implement these steps, you will see a much larger positive from your riding experience. Baddrapp's 650 has aftermarket exhaust, air intake and injector. I'm sure these influenced the final performance I experienced.