I remember a mode on the power commander lll that was supposed to be for race and give instant or quicker throttle response for track use. That leads me to believe the snatchy throttle anomaly was possibly born from some emission requirement to keep the bike lean at off throttle more quickly. This was an option I was given when my bike was professionally tuned by a reputable tuner and performance shop.
One model of the power commander (EX model) does not allow tuning at a specific range so that it can remain emission legal. Because of this, the EX model may not cure your throttle issue.